NAMD-L: By Thread

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NAMD-L: By Thread

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4086 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive

Starting: Mon Jan 02 2012 - 00:44:43 CST
Ending: Tue Dec 31 2013 - 11:28:27 CST

Temperature reassignment PANAGIOTA KYRIAKOU (Tue Dec 31 2013 - 11:28:12 CST)
Add acetyle and amin Group to peptide Alireza Mansouri (Mon Dec 30 2013 - 03:30:19 CST)
- Re: Add acetyle and amin Group to peptide Axel Kohlmeyer (Mon Dec 30 2013 - 03:55:11 CST)
About Namd Compilation Vidhya Sankar (Sat Dec 28 2013 - 11:12:02 CST)
Distance Constraints in ABF Simulation Vince Cho (Wed Dec 25 2013 - 05:31:26 CST)
obtaining the system force Neelanjana Sengupta (Tue Dec 24 2013 - 00:26:59 CST)
- Re: obtaining the system force Giacomo Fiorin (Tue Dec 24 2013 - 10:51:10 CST)
Trouble loading frames from large DCD files Alex Utev (CMP) (Thu Dec 19 2013 - 16:23:30 CST)
- Re: Trouble loading frames from large DCD files Maxim Belkin (Thu Dec 19 2013 - 16:40:27 CST)
- AW: Trouble loading frames from large DCD files Norman Geist (Fri Dec 20 2013 - 01:52:23 CST)
About Membrane anlysis Vidhya Sankar (Wed Dec 18 2013 - 09:09:22 CST)
- Re: About Membrane anlysis Jeffrey Potoff (Wed Dec 18 2013 - 09:50:03 CST)
- Re: About Membrane anlysis Thomas Evangelidis (Wed Dec 18 2013 - 10:45:52 CST)
Problem with replica exchange Michal Skoczek (Tue Dec 17 2013 - 04:57:38 CST)
- AW: Problem with replica exchange Norman Geist (Tue Dec 17 2013 - 05:43:32 CST)
About Free energy tutorial for Membrane-Protein system Vidhya Sankar (Sun Dec 15 2013 - 03:26:34 CST)
minimization with symmetry restrain flavio seixas (Fri Dec 13 2013 - 12:31:39 CST)
- Re: minimization with symmetry restrain JC Gumbart (Fri Dec 13 2013 - 16:48:32 CST)
Will there be a NAMD2.9 for IBM AIX UNIX? Mengyuan Zhu (Fri Dec 13 2013 - 11:06:48 CST)
Reverse coarse-graining Error: CG Builder Sanket Avinash Deshmukh (Fri Dec 13 2013 - 00:42:25 CST)
How to compile NAMD2.9 in IBM AIX UNIX$B!)(B Mengyuan Zhu (Thu Dec 12 2013 - 12:24:42 CST)
Hi Gurpreet Kaur Dhindsa (Thu Dec 12 2013 - 09:19:31 CST)
- Re: Hi Axel Kohlmeyer (Thu Dec 12 2013 - 09:24:31 CST)
Re: AW: vmd-l: AMD vs. nvidia support Aron Broom (Thu Dec 12 2013 - 09:10:52 CST)
- Re: AW: vmd-l: AMD vs. nvidia support Axel Kohlmeyer (Thu Dec 12 2013 - 09:23:37 CST)
AW: vmd-l: AMD vs. nvidia support Norman Geist (Thu Dec 12 2013 - 01:05:22 CST)
membrane bilayer crosses the z axis boundaries of the box and separates into two layers Thomas Evangelidis (Wed Dec 11 2013 - 14:29:33 CST)
colavrs ABF restart not matching Kasra Fattah (Tue Dec 10 2013 - 11:30:50 CST)
- Re: colavrs ABF restart not matching Giacomo Fiorin (Tue Dec 10 2013 - 11:40:38 CST)
  - Re: colavrs ABF restart not matching Kasra Fattah (Tue Dec 10 2013 - 12:02:53 CST)
One Chain Simulation Rawan Al Nsour (Tue Dec 10 2013 - 11:06:10 CST)
- Re: One Chain Simulation Aron Broom (Tue Dec 10 2013 - 11:13:50 CST)
Patch information for 1TUB.pdb in order to use "psfgen" Lili Zhang (Tue Dec 10 2013 - 09:21:39 CST)
- Re: Patch information for 1TUB.pdb in order to use "psfgen" Roy Fernando (Tue Dec 10 2013 - 10:07:22 CST)
puzzle of SMD in NAMD-2.9 and pull code in Gromacs dbaogen (Tue Dec 10 2013 - 06:02:25 CST)
- AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Norman Geist (Tue Dec 10 2013 - 08:18:03 CST)
  - Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs dbaogen (Thu Dec 12 2013 - 19:02:30 CST)
  - Re: Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Aron Broom (Sun Dec 15 2013 - 00:51:33 CST)
- Re: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Axel Kohlmeyer (Tue Dec 10 2013 - 08:22:18 CST)
  - Re: Re: puzzle of SMD in NAMD-2.9 and pull code in Gromacs dbaogen (Tue Dec 10 2013 - 20:27:15 CST)
    - Re: Re: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Axel Kohlmeyer (Wed Dec 11 2013 - 00:02:26 CST)
XY constraints with center of mass movements Peterson J (Mon Dec 09 2013 - 11:29:12 CST)
- Re: XY constraints with center of mass movements Aron Broom (Mon Dec 09 2013 - 12:00:33 CST)
PSF file for a metalloprotein Haleh Abdizadeh (Mon Dec 09 2013 - 07:29:55 CST)
- Re: PSF file for a metalloprotein Roy Fernando (Mon Dec 09 2013 - 09:57:32 CST)
Re: 50% system CPU usage when parallel running NAMD on Rocks cluster ÖÜêÇêÀ (Sun Dec 08 2013 - 09:11:31 CST)
- AW: 50% system CPU usage when parallel running NAMD on Rocks cluster Norman Geist (Mon Dec 09 2013 - 01:19:28 CST)
- Re: 50% system CPU usage when parallel running NAMD on Rocks cluster ÖÜêÇêÀ (Tue Dec 10 2013 - 06:51:31 CST)
  - AW: 50% system CPU usage when parallel running NAMD on Rocks cluster Norman Geist (Tue Dec 10 2013 - 08:19:45 CST)
- Re: 50% system CPU usage when parallel running NAMD on Rocks cluster ÖÜêÇêÀ (Sat Dec 14 2013 - 07:55:47 CST)
  - AW: 50% system CPU usage when parallel running NAMD on Rocks cluster Norman Geist (Mon Dec 16 2013 - 01:07:28 CST)
  - AW: 50% system CPU usage when parallel running NAMD on Rocks cluster Norman Geist (Mon Dec 16 2013 - 01:08:54 CST)
- Re: 50% system CPU usage when parallel running NAMD on Rocks cluster ÖÜêÇêÀ (Tue Dec 17 2013 - 08:12:33 CST)
  - Re: 50% system CPU usage when parallel running NAMD on Rocks cluster Axel Kohlmeyer (Wed Dec 18 2013 - 01:28:34 CST)
    - AW: 50% system CPU usage when parallel running NAMD on Rocks cluster Norman Geist (Wed Dec 18 2013 - 02:06:09 CST)
- Re: 50% system CPU usage when parallel running NAMD on Rocks cluster ÖÜêÇêÀ (Wed Dec 18 2013 - 06:43:18 CST)
  - Re: 50% system CPU usage when parallel running NAMD on Rocks cluster Axel Kohlmeyer (Wed Dec 18 2013 - 07:04:24 CST)
AW: Running NAMD on SGE cluster - multiple modes and cores Norman Geist (Thu Dec 05 2013 - 04:57:18 CST)
Asking for Free energy calculation advice Kasra Fattah (Thu Dec 05 2013 - 14:18:20 CST)
- Re: Asking for Free energy calculation advice Aron Broom (Fri Dec 06 2013 - 11:48:03 CST)
AW: Running NAMD on SGE cluster - multiple modes and cores Norman Geist (Thu Dec 05 2013 - 04:06:31 CST)
AW: Running NAMD on SGE cluster - multiple modes and cores Norman Geist (Thu Dec 05 2013 - 02:58:07 CST)
AW: Running NAMD on SGE cluster - multiple modes and cores Norman Geist (Wed Dec 04 2013 - 07:36:48 CST)
Runaway cuda-enabled namd2 processes Tim.Ho_at_csiro.au (Tue Dec 03 2013 - 21:31:42 CST)
- AW: Runaway cuda-enabled namd2 processes Norman Geist (Wed Dec 04 2013 - 05:41:20 CST)
zeroMomentum for water droplet Mihaela Drenscko (Tue Dec 03 2013 - 17:38:43 CST)
- Re: zeroMomentum for water droplet Axel Kohlmeyer (Tue Dec 03 2013 - 22:38:16 CST)
  - Re: zeroMomentum for water droplet David Hardy (Wed Dec 04 2013 - 09:32:41 CST)
what to do with this error Liqun Zhang (Tue Dec 03 2013 - 14:21:34 CST)
- Re: what to do with this error Pavan (Fri Dec 06 2013 - 08:03:31 CST)
50% system CPU usage when parallel running NAMD on Rocks cluster ÖÜêÇêÀ (Sat Nov 30 2013 - 21:06:18 CST)
Re: Running NAMD on SGE cluster - multiple modes and cores Anna Gorska (Tue Dec 03 2013 - 09:23:30 CST)
- Re: Running NAMD on SGE cluster - multiple modes and cores Anna Gorska (Thu Dec 05 2013 - 05:09:27 CST)
- Re: Running NAMD on SGE cluster - multiple modes and cores Anna Gorska (Thu Dec 05 2013 - 04:14:05 CST)
  - AW: Running NAMD on SGE cluster - multiple modes and cores Norman Geist (Thu Dec 05 2013 - 04:33:12 CST)
- Re: Running NAMD on SGE cluster - multiple modes and cores Anna Gorska (Fri Dec 06 2013 - 07:23:29 CST)
50% system CPU usage when parallel running NAMD on Rocks cluster ÖÜêÇêÀ (Tue Dec 03 2013 - 07:43:07 CST)
- AW: 50% system CPU usage when parallel running NAMD on Rocks cluster Norman Geist (Tue Dec 03 2013 - 08:47:54 CST)
Running NAMD on SGE cluster - multiple modes and cores Anna Gorska (Tue Dec 03 2013 - 05:25:37 CST)
- AW: Running NAMD on SGE cluster - multiple modes and cores Norman Geist (Tue Dec 03 2013 - 06:12:08 CST)
Re: ÅÙÇÏÉ ÊèÌêç: Mamon Hatmal (Tue Dec 03 2013 - 05:14:42 CST)
restrain noe's in random.inp Vanessa Gameiro (Tue Dec 03 2013 - 04:12:38 CST)
Reduce percent use of cpu jafar azamat (Tue Dec 03 2013 - 02:31:53 CST)
Bug in T-REMD with colvars Francesco Pietra (Tue Dec 03 2013 - 01:55:14 CST)
- Fwd: Bug in T-REMD with colvars Francesco Pietra (Tue Dec 03 2013 - 02:55:43 CST)
  - Fwd: Bug in T-REMD with colvars Francesco Pietra (Tue Dec 03 2013 - 13:31:24 CST)
AW: BUG: TCL coorfile command Norman Geist (Mon Dec 02 2013 - 01:43:41 CST)
pH calculation Nadia Salami (Sun Dec 01 2013 - 23:31:02 CST)
- Re: pH calculation JÃ©rÃ´me HÃ©nin (Mon Dec 02 2013 - 03:05:46 CST)
charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program" Frank Thommen (Sat Nov 30 2013 - 14:51:55 CST)
- AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program" Norman Geist (Mon Dec 02 2013 - 02:05:24 CST)
  - Re: AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program" Frank Thommen (Mon Dec 02 2013 - 04:07:42 CST)
    - AW: AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program" Norman Geist (Mon Dec 02 2013 - 05:27:37 CST)
Colvars periodic boundary treatment question Kasra Fattah (Sat Nov 30 2013 - 13:12:42 CST)
- Re: Colvars periodic boundary treatment question JÃ©rÃ´me HÃ©nin (Sat Nov 30 2013 - 19:04:48 CST)
  - Re: Colvars periodic boundary treatment question Kasra Fattah (Sat Nov 30 2013 - 22:25:46 CST)
Phosphorylating a residue with Amber ff Charles McAnany (Sat Nov 30 2013 - 12:24:19 CST)
- Re: Phosphorylating a residue with Amber ff vapour (Tue Dec 03 2013 - 17:29:31 CST)
Modify Molecule.C to avoid fatal error? George Patargias (Thu Nov 28 2013 - 02:26:37 CST)
Drifting water molecules Mihaela Drenscko (Wed Nov 27 2013 - 16:45:10 CST)
- Re: Drifting water molecules Axel Kohlmeyer (Wed Nov 27 2013 - 16:56:17 CST)
  - AW: Drifting water molecules Norman Geist (Thu Nov 28 2013 - 02:59:56 CST)
    - Re: AW: Drifting water molecules Axel Kohlmeyer (Thu Nov 28 2013 - 04:17:47 CST)
Error with dummy atoms George Patargias (Wed Nov 27 2013 - 11:07:40 CST)
Problem regarding the Pre-Minimizer Bad Contacts Removal Norman Geist (Wed Nov 27 2013 - 02:24:28 CST)
xplor psf used for namd Jana, Suvamay (Mon Nov 25 2013 - 20:07:31 CST)
can i use swap partition to increase ram in namd? k.manzoorolajdad (Mon Nov 25 2013 - 09:18:15 CST)
- Re: can i use swap partition to increase ram in namd? Axel Kohlmeyer (Mon Nov 25 2013 - 09:26:13 CST)
inconsistency between "Benchmark" and "Timing" output Vlad Cojocaru (Mon Nov 25 2013 - 09:08:58 CST)
- AW: inconsistency between "Benchmark" and "Timing" output Norman Geist (Tue Nov 26 2013 - 01:08:31 CST)
Sherical BC energy conservation Norman Geist (Mon Nov 25 2013 - 03:18:37 CST)
diffusion of protein into water box Ramin Ekhteiari (Sun Nov 24 2013 - 08:06:27 CST)
- Re: diffusion of protein into water box Axel Kohlmeyer (Sun Nov 24 2013 - 08:14:52 CST)
  - Re: diffusion of protein into water box Ramin Ekhteiari (Sun Nov 24 2013 - 08:21:04 CST)
Fwd: manish kesherwani (Sun Nov 24 2013 - 06:29:35 CST)
Carma v.1.3 available for download Nicholas M Glykos (Sun Nov 24 2013 - 04:33:05 CST)
Interaction energy definition nan li (Fri Nov 22 2013 - 14:45:13 CST)
- Re: Interaction energy definition Aron Broom (Fri Nov 22 2013 - 14:57:35 CST)
  - Re: Interaction energy definition nan li (Fri Nov 22 2013 - 15:21:31 CST)
    - Re: Interaction energy definition Aron Broom (Sat Nov 23 2013 - 07:09:54 CST)
(no subject) sutapa dutta (Fri Nov 22 2013 - 05:04:36 CST)
New empirical force field tools: Release of R.E.D. Server Dev./R.E.D. Python FyD (Fri Nov 22 2013 - 04:18:53 CST)
pre residues and ligands interaction Ramin Ekhteiari (Thu Nov 21 2013 - 06:48:15 CST)
- Re: pre residues and ligands interaction Axel Kohlmeyer (Thu Nov 21 2013 - 06:55:04 CST)
How to apply Symmetry boundary on NAMD zhangxing (Tue Nov 19 2013 - 17:52:50 CST)
How to replace NAMD electrostatics Juba, Derek (Tue Nov 19 2013 - 16:36:20 CST)
- Re: How to replace NAMD electrostatics Axel Kohlmeyer (Tue Nov 19 2013 - 16:53:01 CST)
- Re: How to replace NAMD electrostatics Axel Kohlmeyer (Tue Nov 19 2013 - 16:54:29 CST)
  - Re: How to replace NAMD electrostatics Aron Broom (Tue Nov 19 2013 - 17:00:16 CST)
NAMD_2.9_Linux-x86_64-ibverbs RUNS on QueenBee RUN TIME VARIATION Thomas C. Bishop (Tue Nov 19 2013 - 08:06:31 CST)
- AW: NAMD_2.9_Linux-x86_64-ibverbs RUNS on QueenBee RUN TIME VARIATION Norman Geist (Tue Nov 19 2013 - 09:07:42 CST)
Approaching Deadline December 1st 2013 - Advanced LAMMPS and Scientific Software Development Workshop at ICTP in March 2014 Axel Kohlmeyer (Tue Nov 19 2013 - 03:46:45 CST)
Compile NAMD with FFTW3 and MPI Chan Tabris C (Tue Nov 19 2013 - 02:45:00 CST)
- Re: Compile NAMD with FFTW3 and MPI Axel Kohlmeyer (Tue Nov 19 2013 - 02:50:48 CST)
ABF calculations in NAMD Johny Telecaster (Mon Nov 18 2013 - 07:36:58 CST)
Question about how much used from CPU? jafar azamat (Mon Nov 18 2013 - 02:50:14 CST)
- AW: Question about how much used from CPU? Norman Geist (Tue Nov 19 2013 - 03:06:14 CST)
Adaptive tempering exception error Matthew Ralph Adendorff (Sun Nov 17 2013 - 09:52:27 CST)
Re: PCIexpress 3.0 for MD with NAMD on GPUs Thomas Albers (Sat Nov 16 2013 - 09:58:22 CST)
- Re: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Sun Nov 17 2013 - 04:56:04 CST)
  - Fwd: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Sun Nov 17 2013 - 09:06:51 CST)
Steered MD along detected routes Johny Telecaster (Sat Nov 16 2013 - 05:10:40 CST)
- Re: Steered MD along detected routes Munir S. Skaf (Sat Nov 16 2013 - 06:43:08 CST)
  - Re: Steered MD along detected routes Johny Telecaster (Sat Nov 16 2013 - 10:27:38 CST)
    - Re: Steered MD along detected routes Johny Telecaster (Sat Nov 16 2013 - 10:46:01 CST)
    - Re: Steered MD along detected routes Johny Telecaster (Sat Nov 16 2013 - 10:48:42 CST)
FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Fri Nov 15 2013 - 14:41:13 CST)
FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Fri Nov 15 2013 - 15:02:06 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Mon Nov 18 2013 - 11:44:59 CST)
  - Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Mon Nov 18 2013 - 12:56:19 CST)
problem of using SMD and TclForces keywords simultaneously dbaogen (Fri Nov 15 2013 - 02:42:07 CST)
Re: NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ? Axel Kohlmeyer (Thu Nov 14 2013 - 06:52:52 CST)
AW: Separate water coordinates from graphite Norman Geist (Thu Nov 14 2013 - 06:34:46 CST)
NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ? Nicolas Floquet (Thu Nov 14 2013 - 05:17:48 CST)
- AW: NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ? Norman Geist (Thu Nov 14 2013 - 06:43:49 CST)
AW: Separate water coordinates from graphite Norman Geist (Thu Nov 14 2013 - 01:26:31 CST)
Release of ConcatXY Ali Khanlarkhani (Tue Nov 12 2013 - 16:18:36 CST)
Separate water coordinates from graphite Mihaela Drenscko (Tue Nov 12 2013 - 13:57:01 CST)
- AW: Separate water coordinates from graphite Norman Geist (Wed Nov 13 2013 - 04:58:35 CST)
Steered Molecular Dynamics tutorial James Starlight (Tue Nov 12 2013 - 03:40:44 CST)
- Re: Steered Molecular Dynamics tutorial James Starlight (Wed Nov 13 2013 - 12:11:57 CST)
Fwd: RE: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Tue Nov 12 2013 - 01:46:45 CST)
- RE: RE: PCIexpress 3.0 for MD with NAMD on GPUs Lane, William (Fri Nov 15 2013 - 02:22:53 CST)
Re: TclForces and efficient PBC corrections Axel Kohlmeyer (Tue Nov 12 2013 - 01:32:28 CST)
- AW: TclForces and efficient PBC corrections Norman Geist (Tue Nov 12 2013 - 01:55:16 CST)
Why does my volume suddenly expand as I increase temperature. Martin, Erik W (Mon Nov 11 2013 - 17:55:05 CST)
- Re: Why does my volume suddenly expand as I increase temperature. Aron Broom (Mon Nov 11 2013 - 19:12:33 CST)
  - AW: Why does my volume suddenly expand as I increase temperature. Norman Geist (Tue Nov 12 2013 - 01:23:47 CST)
    - RE: Why does my volume suddenly expand as I increase temper ature.. . Martin, Erik W (Tue Nov 12 2013 - 09:14:29 CST)
TclForces and efficient PBC corrections Morgan, Brittany (Mon Nov 11 2013 - 12:02:52 CST)
- AW: TclForces and efficient PBC corrections Norman Geist (Tue Nov 12 2013 - 01:19:01 CST)
  - RE: TclForces and efficient PBC corrections Morgan, Brittany (Wed Nov 13 2013 - 10:31:31 CST)
- Re: TclForces and efficient PBC corrections Axel Kohlmeyer (Tue Nov 12 2013 - 01:37:53 CST)
PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Mon Nov 11 2013 - 03:51:02 CST)
Poor scaling in NAMD simulations Tristan Croll (Fri Nov 08 2013 - 22:11:41 CST)
BLCR and NAMD Phil Miller (Thu Nov 07 2013 - 22:47:14 CST)
- Re: BLCR and NAMD Joseph Farran (Thu Nov 07 2013 - 22:56:44 CST)
- Re: BLCR and NAMD Paul Hargrove (Fri Nov 08 2013 - 01:54:48 CST)
pairInteractionSelf interaction terms Christopher Von Bargen (Thu Nov 07 2013 - 15:22:58 CST)
Namd energy plugin James Starlight (Thu Nov 07 2013 - 01:53:52 CST)
Force Field Parameters for PEG Roy Fernando (Wed Nov 06 2013 - 12:21:46 CST)
- Re: Force Field Parameters for PEG Kenno Vanommeslaeghe (Wed Nov 06 2013 - 13:27:41 CST)
  - Re: Force Field Parameters for PEG Roy Fernando (Wed Nov 06 2013 - 13:58:57 CST)
MM-PBSA calculation Ramin Ekhteiari (Wed Nov 06 2013 - 02:56:43 CST)
- Re: MM-PBSA calculation Hannes Loeffler (Wed Nov 06 2013 - 03:25:23 CST)
Re: Accelerated MD in NAMD James Starlight (Wed Nov 06 2013 - 01:29:53 CST)
- Re: Accelerated MD in NAMD Jeff Wereszczynski (Wed Nov 06 2013 - 12:00:29 CST)
  - Re: Accelerated MD in NAMD James Starlight (Wed Nov 06 2013 - 12:50:36 CST)
- Re: Accelerated MD in NAMD James Starlight (Fri Nov 08 2013 - 00:53:41 CST)
  - Re: Accelerated MD in NAMD James Starlight (Fri Nov 08 2013 - 06:36:51 CST)
Equilibration of the membrane-protein system done in CHARMM-GUI James Starlight (Wed Nov 06 2013 - 00:51:22 CST)
- Re: Equilibration of the membrane-protein system done in CHARMM-GUI Sunhwan Jo (Wed Nov 06 2013 - 08:07:25 CST)
  - Re: Equilibration of the membrane-protein system done in CHARMM-GUI James Starlight (Wed Nov 06 2013 - 09:02:45 CST)
Re: FEP simulation: protein moving out of water box. Niklaus Johner (Tue Nov 05 2013 - 21:21:48 CST)
FEP simulation: protein moving out of water box. venkata agasthya (Tue Nov 05 2013 - 19:39:51 CST)
accelerated MD and External Electric Field Thomas Evangelidis (Tue Nov 05 2013 - 07:10:24 CST)
Potential energy in the boundaries Nadia Salami (Tue Nov 05 2013 - 03:06:50 CST)
regarding editing protonated glutamate in the pdb file via psfgen Prathit Chatterjee (Tue Nov 05 2013 - 00:53:17 CST)
- RE: regarding editing protonated glutamate in the pdb file via psfgen . . Martin, Erik W (Tue Nov 05 2013 - 01:38:20 CST)
Restarting T-REMD with colvars Francesco Pietra (Mon Nov 04 2013 - 10:19:30 CST)
- Fwd: Restarting T-REMD with colvars Francesco Pietra (Tue Nov 05 2013 - 01:48:45 CST)
  - Fwd: Restarting T-REMD with colvars Francesco Pietra (Tue Nov 05 2013 - 01:53:50 CST)
    - Re: Restarting T-REMD with colvars Francesco Pietra (Tue Nov 05 2013 - 13:58:55 CST)
Re: Using volmap to calculate the water density around certain residues bharat gupta (Mon Nov 04 2013 - 02:25:22 CST)
- Re: Re: Using volmap to calculate the water density around certain residues Axel Kohlmeyer (Mon Nov 04 2013 - 02:32:22 CST)
Accelerated MD in NAMD James Starlight (Sun Nov 03 2013 - 08:17:51 CST)
About Psfgen for cyclic peptide Vidhya Sankar (Sun Nov 03 2013 - 00:08:11 CDT)
simulation crashes frequently with "atoms moving too fast" eprates_at_iqm.unicamp.br (Fri Nov 01 2013 - 16:26:57 CDT)
- Martini RBCG simulation frequently crashing with "atoms moving too fast" eprates_at_iqm.unicamp.br (Sun Nov 03 2013 - 11:57:18 CST)
  - AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" Norman Geist (Mon Nov 04 2013 - 01:17:46 CST)
Problem in creating dummy atom Atanu Maity (Fri Nov 01 2013 - 01:43:09 CDT)
Charge distribution Peterson J (Fri Nov 01 2013 - 00:28:34 CDT)
- Re: Charge distribution Kenno Vanommeslaeghe (Fri Nov 01 2013 - 13:52:54 CDT)
Extract KE, PE and total energy from log file Mihaela Drenscko (Thu Oct 31 2013 - 15:15:04 CDT)
- Re: Extract KE, PE and total energy from log file Aron Broom (Thu Oct 31 2013 - 15:39:05 CDT)
  - Re: Extract KE, PE and total energy from log file Ajasja LjubetiÄ (Thu Oct 31 2013 - 18:05:37 CDT)
- Re: Extract KE, PE and total energy from log file Mihaela Drenscko (Sat Nov 02 2013 - 17:49:06 CDT)
  - AW: Extract KE, PE and total energy from log file Norman Geist (Mon Nov 04 2013 - 01:13:05 CST)
accelerated MD parameters for dual boost mode Huihui Liu (Thu Oct 31 2013 - 10:04:23 CDT)
HMMM model Tristan Croll (Wed Oct 30 2013 - 22:51:50 CDT)
HEME B PARAMETERS Sadegh Faramarzi Ganjabad (Wed Oct 30 2013 - 02:30:09 CDT)
- Re: HEME B PARAMETERS Kenno Vanommeslaeghe (Thu Oct 31 2013 - 13:06:26 CDT)
I have a question about pair interaction energy calculations. ¼Û ¿¬È£ (Wed Oct 30 2013 - 02:14:32 CDT)
- Re: I have a question about pair interaction energy calculations. Kenno Vanommeslaeghe (Thu Oct 31 2013 - 13:21:31 CDT)
reassignTemp question Martin, Erik W (Tue Oct 29 2013 - 15:26:46 CDT)
- Re: reassignTemp question Aron Broom (Tue Oct 29 2013 - 15:40:46 CDT)
  - Re: reassignTemp question Ajasja LjubetiÄ (Tue Oct 29 2013 - 16:26:41 CDT)
    - Re: reassignTemp question Aron Broom (Tue Oct 29 2013 - 16:44:52 CDT)
    - Re: reassignTemp question Martin, Erik W (Tue Oct 29 2013 - 18:55:08 CDT)
FEP Error - TCL Eudes Fileti (Tue Oct 29 2013 - 14:28:17 CDT)
- Re: FEP Error - TCL JÃ©rÃ´me HÃ©nin (Wed Oct 30 2013 - 11:07:33 CDT)
  - Re: FEP Error - TCL JÃ©rÃ´me HÃ©nin (Tue Nov 12 2013 - 16:17:13 CST)
unsuscribe Rehan Zafar (Tue Oct 29 2013 - 11:30:35 CDT)
unsuscribe Cat Chenal (Tue Oct 29 2013 - 09:45:33 CDT)
AW: vmd-l: Creating custom molecule in VMD scripting Norman Geist (Tue Oct 29 2013 - 07:16:46 CDT)
Re: Namd options from TCL Ajasja LjubetiÄ (Tue Oct 29 2013 - 04:44:50 CDT)
Two GPU-based workstation James Starlight (Tue Oct 29 2013 - 00:29:43 CDT)
- Re: Two GPU-based workstation Shubhra Ghosh Dastidar (Tue Oct 29 2013 - 01:53:16 CDT)
ABF: Distances in colvars.traj not identical with VMD exported distances Maximilian Ebert (Mon Oct 28 2013 - 16:21:45 CDT)
- Re: ABF: Distances in colvars.traj not identical with VMD exported distances Giacomo Fiorin (Mon Oct 28 2013 - 16:28:15 CDT)
  - Re: ABF: Distances in colvars.traj not identical with VMD exported distances Maximilian Ebert (Tue Oct 29 2013 - 07:13:04 CDT)
    - Re: ABF: Distances in colvars.traj not identical with VMD exported distances Giacomo Fiorin (Tue Oct 29 2013 - 09:33:36 CDT)
    - Re: ABF: Distances in colvars.traj not identical with VMD exported distances Maximilian Ebert (Tue Oct 29 2013 - 10:02:05 CDT)
PLUMED 2.0 announcement Massimiliano Bonomi (Mon Oct 28 2013 - 06:51:47 CDT)
Mysterious slow down in parallel Roy Fernando (Sat Oct 26 2013 - 10:05:13 CDT)
- Re: Mysterious slow down in parallel Axel Kohlmeyer (Sat Oct 26 2013 - 17:04:11 CDT)
  - Re: Mysterious slow down in parallel Roy Fernando (Sat Oct 26 2013 - 22:06:49 CDT)
AW: Re: DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface Norman Geist (Thu Oct 24 2013 - 11:53:37 CDT)
Calculating pressure on each direction Bala subramanian (Thu Oct 24 2013 - 07:53:07 CDT)
- Re: Calculating pressure on each direction Bala subramanian (Thu Oct 24 2013 - 10:25:20 CDT)
Mac OS Binary for NAMD 2.10 Eudes Fileti (Thu Oct 24 2013 - 06:16:31 CDT)
DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface Norman Geist (Thu Oct 24 2013 - 01:21:19 CDT)
- Re: DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface Jim Phillips (Thu Oct 24 2013 - 10:01:30 CDT)
  - AW: Re: DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface Norman Geist (Thu Oct 24 2013 - 11:51:38 CDT)
  - AW: Re: DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface Norman Geist (Mon Oct 28 2013 - 09:17:36 CDT)
NAMD and water models Mihaela Drenscko (Wed Oct 23 2013 - 20:13:17 CDT)
- Re: NAMD and water models Axel Kohlmeyer (Wed Oct 23 2013 - 23:22:16 CDT)
Fwd: Re: [Checkpoint] BLCR and NAMD Joseph Farran (Wed Oct 23 2013 - 13:46:00 CDT)
- Re: Fwd: Re: [Checkpoint] BLCR and NAMD Joseph Farran (Fri Oct 25 2013 - 12:33:29 CDT)
Bonds in XPLOR format Mihaela Drenscko (Wed Oct 23 2013 - 13:00:05 CDT)
- Re: Bonds in XPLOR format David Hardy (Wed Oct 23 2013 - 13:14:23 CDT)
- Re: Bonds in XPLOR format Mihaela Drenscko (Wed Oct 23 2013 - 13:23:10 CDT)
  - Re: Bonds in XPLOR format Sunhwan Jo (Wed Oct 23 2013 - 13:28:27 CDT)
  - Re: Bonds in XPLOR format Kenno Vanommeslaeghe (Wed Oct 23 2013 - 13:49:24 CDT)
Membrane/peptide system. Water moving from one layer to the other ... Villalain Boullon, Jose (Wed Oct 23 2013 - 05:46:00 CDT)
- Re: Membrane/peptide system. Water moving from one layer to the other ... Ajasja LjubetiÄ (Wed Oct 23 2013 - 07:30:36 CDT)
NAMD Internal energy unit Norman Geist (Wed Oct 23 2013 - 05:16:57 CDT)
Namd options from TCL Norman Geist (Tue Oct 22 2013 - 10:26:37 CDT)
AW: Fixed and SMD atoms Norman Geist (Tue Oct 22 2013 - 03:37:09 CDT)
MMPBSA-like analysis Revthi Sanker (Tue Oct 22 2013 - 02:04:49 CDT)
- Re: MMPBSA-like analysis Peter Jones (Tue Oct 22 2013 - 04:21:24 CDT)
Method for solvation of protein Xingcheng Lin (Mon Oct 21 2013 - 15:45:16 CDT)
- Re: Method for solvation of protein Dong Luo (Tue Oct 22 2013 - 10:57:17 CDT)
[OT] A new method for quantifying convergence of MD simulations Nicholas M Glykos (Mon Oct 21 2013 - 12:37:45 CDT)
Re: vmd-l: fftk-charges rodolfo gonzalez (Mon Oct 21 2013 - 01:57:55 CDT)
- Re: Re: vmd-l: fftk-charges Kenno Vanommeslaeghe (Mon Oct 21 2013 - 12:53:59 CDT)
AW: vmd-l: fftk-charges Norman Geist (Mon Oct 21 2013 - 01:23:48 CDT)
Fixed and SMD atoms Mihaela Drenscko (Sat Oct 19 2013 - 14:16:47 CDT)
- AW: Fixed and SMD atoms Norman Geist (Mon Oct 21 2013 - 01:37:28 CDT)
Simulation results from NVT has a cavity Xingcheng Lin (Sat Oct 19 2013 - 13:49:12 CDT)
- Re: Simulation results from NVT has a cavity Kenno Vanommeslaeghe (Mon Oct 21 2013 - 12:25:58 CDT)
Adaptive tempering floating point exception Stober, Spencer T (Fri Oct 18 2013 - 13:21:03 CDT)
CUDA vd non-CUDA for minimization Francesco Pietra (Fri Oct 18 2013 - 12:13:04 CDT)
- Re: CUDA vd non-CUDA for minimization Kenno Vanommeslaeghe (Fri Oct 18 2013 - 13:55:00 CDT)
  - Re: CUDA vd non-CUDA for minimization Francesco Pietra (Sat Oct 19 2013 - 02:28:50 CDT)
    - Re: CUDA vd non-CUDA for minimization Kenno Vanommeslaeghe (Mon Oct 21 2013 - 11:34:26 CDT)
Re: [SUSPICIOUS MESSAGE] Reg System Prepartion namd Kenno Vanommeslaeghe (Thu Oct 17 2013 - 16:15:10 CDT)
Running NAMD in multiprocessor single machine Roy Fernando (Thu Oct 17 2013 - 16:02:58 CDT)
- Re: Running NAMD in multiprocessor single machine Roy Fernando (Thu Oct 17 2013 - 16:28:02 CDT)
  - Re: Running NAMD in multiprocessor single machine Aron Broom (Thu Oct 17 2013 - 19:31:20 CDT)
Peptide insertion into a membrane Villalain Boullon, Jose (Thu Oct 17 2013 - 07:44:47 CDT)
- Re: Peptide insertion into a membrane Kenno Vanommeslaeghe (Thu Oct 17 2013 - 15:08:10 CDT)
  - Re: Peptide insertion into a membrane Lucas (Thu Oct 17 2013 - 17:33:38 CDT)
Error Mihaela Drenscko (Wed Oct 16 2013 - 20:15:29 CDT)
- Re: Error Kenno Vanommeslaeghe (Wed Oct 16 2013 - 21:21:20 CDT)
  - AW: Error Norman Geist (Thu Oct 17 2013 - 00:38:22 CDT)
  - Re: Error Kenno Vanommeslaeghe (Mon Oct 21 2013 - 12:17:41 CDT)
get topology and parameter file for the ligand. Ramin Ekhteiari (Wed Oct 16 2013 - 12:14:15 CDT)
- Re: get topology and parameter file for the ligand. Kenno Vanommeslaeghe (Wed Oct 16 2013 - 17:21:38 CDT)
NAMD build problems on PowerPC under Red Hat Enterprise Lane, William (Wed Oct 16 2013 - 11:37:12 CDT)
Pass a runtime parameter into the configuration file Xingcheng Lin (Tue Oct 15 2013 - 17:55:48 CDT)
- AW: Pass a runtime parameter into the configuration file Norman Geist (Wed Oct 16 2013 - 00:45:18 CDT)
NAMD simulation with flag similar to -maxh in Gromacs Xingcheng Lin (Tue Oct 15 2013 - 11:30:49 CDT)
- Re: NAMD simulation with flag similar to -maxh in Gromacs Dong Luo (Tue Oct 15 2013 - 11:50:45 CDT)
About Constraint Failure Vidhya Sankar (Tue Oct 15 2013 - 04:57:04 CDT)
- Re: About Constraint Failure Kenno Vanommeslaeghe (Tue Oct 15 2013 - 12:33:23 CDT)
  - AW: About Constraint Failure Norman Geist (Wed Oct 16 2013 - 00:31:03 CDT)
Combining several proteins of the same type together Lili Zhang (Mon Oct 14 2013 - 13:54:56 CDT)
question about NAMD on Kraken. Martin, Erik W (Mon Oct 14 2013 - 13:44:10 CDT)
Protein-ligand affinity James Starlight (Mon Oct 14 2013 - 13:20:17 CDT)
- Re: Protein-ligand affinity Aron Broom (Mon Oct 14 2013 - 22:16:00 CDT)
  - Re: Protein-ligand affinity James Starlight (Tue Oct 15 2013 - 12:42:09 CDT)
question about setting up FEP calculations Shyno Mathew (Mon Oct 14 2013 - 10:48:46 CDT)
- Re: question about setting up FEP calculations JÃ©rÃ´me HÃ©nin (Mon Oct 14 2013 - 14:32:34 CDT)
  - Re: question about setting up FEP calculations Shyno Mathew (Mon Oct 14 2013 - 20:01:48 CDT)
rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs Thomas C. Bishop (Sun Oct 13 2013 - 22:29:51 CDT)
- AW: rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs Norman Geist (Mon Oct 14 2013 - 01:15:13 CDT)
About Usage of Topolgy and Parameter Vidhya Sankar (Sun Oct 13 2013 - 06:59:39 CDT)
- Re: About Usage of Topolgy and Parameter Kenno Vanommeslaeghe (Mon Oct 14 2013 - 00:26:01 CDT)
  - Re: About Usage of Topolgy and Parameter Vidhya Sankar (Mon Oct 14 2013 - 08:24:20 CDT)
    - Re: About Usage of Topolgy and Parameter Kenno Vanommeslaeghe (Mon Oct 14 2013 - 11:09:59 CDT)
BUG Report: NAMD 2.10 Nightly Build from 11.Sep Norman Geist (Fri Oct 11 2013 - 06:23:14 CDT)
Reg Lack of Lack of VDW parameters Vidhya Sankar (Wed Oct 09 2013 - 10:57:58 CDT)
AW: vmd-l: Finding particles that are close Norman Geist (Tue Oct 08 2013 - 06:48:07 CDT)
Simulation of a protein and ions Stephan Matthias Grein (Tue Oct 08 2013 - 03:29:05 CDT)
Simulation of a protein and calcium ions Stephan Matthias Grein (Tue Oct 08 2013 - 03:15:44 CDT)
- Re: Simulation of a protein and calcium ions Ajasja LjubetiÄ (Tue Oct 08 2013 - 03:29:28 CDT)
  - Re: Simulation of a protein and calcium ions Ajasja LjubetiÄ (Tue Oct 08 2013 - 04:08:56 CDT)
    - Re: Simulation of a protein and calcium ions Stephan Matthias Grein (Tue Oct 08 2013 - 04:49:53 CDT)
    - Re: Simulation of a protein and calcium ions Ajasja LjubetiÄ (Tue Oct 08 2013 - 08:21:38 CDT)
- Re: Simulation of a protein and calcium ions Axel Kohlmeyer (Tue Oct 08 2013 - 03:29:40 CDT)
- Re: Simulation of a protein and calcium ions Kenno Vanommeslaeghe (Tue Oct 08 2013 - 11:37:19 CDT)
  - Re: Simulation of a protein and calcium ions Stephan Matthias Grein (Wed Oct 09 2013 - 02:39:27 CDT)
    - Re: Simulation of a protein and calcium ions Axel Kohlmeyer (Wed Oct 09 2013 - 02:45:01 CDT)
abf integrate on two dimensional pmf Nadeem A. Vellore (Mon Oct 07 2013 - 21:25:11 CDT)
- Re: abf integrate on two dimensional pmf Ajasja LjubetiÄ (Tue Oct 08 2013 - 03:20:52 CDT)
Accumulating free energy change for applying colvar restraint Randy J. Zauhar (Mon Oct 07 2013 - 08:50:07 CDT)
- Re: Accumulating free energy change for applying colvar restraint JÃ©rÃ´me HÃ©nin (Mon Oct 07 2013 - 09:06:15 CDT)
How I can to change the force field function in NAMD for protein phi-value analysis Juan José Galano Frutos (Mon Oct 07 2013 - 04:55:44 CDT)
- Re: How I can to change the force field function in NAMD for protein phi-value analysis Giacomo Fiorin (Mon Oct 07 2013 - 08:30:34 CDT)
  - Re: How I can to change the force field function in NAMD for protein phi-value analysis Felipe Merino (Mon Oct 07 2013 - 09:15:48 CDT)
Lennard Jones (LJ) parameters Bachir Aoun (Sun Oct 06 2013 - 15:23:36 CDT)
- Re: Lennard Jones (LJ) parameters Axel Kohlmeyer (Sun Oct 06 2013 - 15:36:22 CDT)
problem with Dihedral farzad kiani (Sun Oct 06 2013 - 07:27:01 CDT)
- Re: problem with Dihedral Kenno Vanommeslaeghe (Sun Oct 06 2013 - 21:42:57 CDT)
(no subject) buksanbio_at_gmail.com (Sat Oct 05 2013 - 16:12:07 CDT)
About restaring Simulation Vidhya Sankar (Sat Oct 05 2013 - 02:56:01 CDT)
- Re: About restaring Simulation Aron Broom (Sat Oct 05 2013 - 07:10:17 CDT)
.psf file in VMD Lili Zhang (Thu Oct 03 2013 - 12:10:56 CDT)
Biotin force field Zack Scholl (Thu Oct 03 2013 - 10:44:25 CDT)
- Re: Biotin force field Kenno Vanommeslaeghe (Thu Oct 03 2013 - 13:28:51 CDT)
Problem in SMD "Constant Velocity Pulling" on Ubiquitin example Lili Zhang (Thu Oct 03 2013 - 08:53:48 CDT)
simultaneous simulation for protein in water and SMD amit banerjee (Thu Oct 03 2013 - 07:33:04 CDT)
- Re: simultaneous simulation for protein in water and SMD Axel Kohlmeyer (Thu Oct 03 2013 - 07:39:03 CDT)
  - Re: simultaneous simulation for protein in water and SMD amit banerjee (Thu Oct 03 2013 - 12:36:23 CDT)
    - Re: simultaneous simulation for protein in water and SMD Axel Kohlmeyer (Thu Oct 03 2013 - 12:40:05 CDT)
    - Re: simultaneous simulation for protein in water and SMD Aron Broom (Thu Oct 03 2013 - 13:02:55 CDT)
MD- GPU Sagar Gore (Thu Oct 03 2013 - 06:51:02 CDT)
- Re: MD- GPU Aron Broom (Thu Oct 03 2013 - 07:06:24 CDT)
membrane protein simulation lipid bilayer question Tian Li (Wed Oct 02 2013 - 19:48:35 CDT)
Problem in running "Constant Velocity Pulling" example Lili Zhang (Wed Oct 02 2013 - 12:25:56 CDT)
Questions regarding pressure difference houyang chen (Wed Oct 02 2013 - 08:29:43 CDT)
Extent of Sampling possible using classical all-atom MD Simulations Aditya Ranganathan (Tue Oct 01 2013 - 08:22:42 CDT)
Same NAMD files give error in Linux but not in Windows .... Villalain Boullon, Jose (Tue Oct 01 2013 - 03:49:55 CDT)
- Re: Same NAMD files give error in Linux but not in Windows .... Axel Kohlmeyer (Tue Oct 01 2013 - 03:54:56 CDT)
TOTLAL2, POTENTIAL abd aMD sunyeping (Mon Sep 30 2013 - 03:11:43 CDT)
questions regarding pressure difference houyang chen (Sun Sep 29 2013 - 22:55:10 CDT)
reg Parameters Vidhya Sankar (Sun Sep 29 2013 - 08:35:10 CDT)
- Re: reg Parameters Kenno Vanommeslaeghe (Sun Sep 29 2013 - 14:11:14 CDT)
Reg Reading of files durin simulation Vidhya Sankar (Sat Sep 28 2013 - 03:52:32 CDT)
NAMD_multiprocessor Shomesankar Bhunia (Sat Sep 28 2013 - 03:08:23 CDT)
- Re: NAMD_multiprocessor Shomesankar Bhunia (Sat Sep 28 2013 - 03:15:11 CDT)
  - Re: NAMD_multiprocessor Ramin Ekhteiari (Sat Sep 28 2013 - 04:40:19 CDT)
Reg VDw Parameters Vidhya Sankar (Fri Sep 27 2013 - 11:18:30 CDT)
- Re: Reg VDw Parameters Kenno Vanommeslaeghe (Fri Sep 27 2013 - 13:36:47 CDT)
Adaptive tempering floating point exception Stober, Spencer T (Fri Sep 27 2013 - 09:56:10 CDT)
(no subject) Arman Imen (Thu Sep 26 2013 - 05:49:15 CDT)
AW: vmd-l: non-orthorhombic PBCs Norman Geist (Thu Sep 26 2013 - 00:49:18 CDT)
AW: Coordinates of Carbon atoms on Graphite Norman Geist (Thu Sep 26 2013 - 00:45:38 CDT)
Re: cell origin problem Haleh Abdizadeh (Wed Sep 25 2013 - 14:00:49 CDT)
- Re: cell origin problem Aron Broom (Wed Sep 25 2013 - 14:53:19 CDT)
  - Re: cell origin problem Haleh Abdizadeh (Wed Sep 25 2013 - 15:06:19 CDT)
- AW: cell origin problem Norman Geist (Thu Sep 26 2013 - 00:59:57 CDT)
lone pair velocities Gergely Gyimesi (Wed Sep 25 2013 - 11:27:48 CDT)
Gold nanoparticle Dr. Eddie (Wed Sep 25 2013 - 11:25:45 CDT)
- Re: Gold nanoparticle Axel Kohlmeyer (Wed Sep 25 2013 - 11:34:39 CDT)
  - Re: Gold nanoparticle Dr. Eddie (Wed Sep 25 2013 - 11:52:48 CDT)
NAMD electrostatic interaction Failure MEHRAN MB (Wed Sep 25 2013 - 10:53:25 CDT)
NAMD electrostatic interaction Failure. Mehran Bagheri (Wed Sep 25 2013 - 08:58:03 CDT)
- Re: NAMD electrostatic interaction Failure. Kenno Vanommeslaeghe (Wed Sep 25 2013 - 19:32:11 CDT)
  - Re: NAMD electrostatic interaction Failure. Mehran MB (Thu Sep 26 2013 - 10:12:16 CDT)
    - Re: NAMD electrostatic interaction Failure. Kenno Vanommeslaeghe (Thu Sep 26 2013 - 16:59:20 CDT)
    - Re: NAMD electrostatic interaction Failure. MEHRAN MB (Thu Sep 26 2013 - 17:27:31 CDT)
AW: Coordinates of Carbon atoms on Graphite Norman Geist (Wed Sep 25 2013 - 09:16:24 CDT)
AW: Coordinates of Carbon atoms on Graphite Norman Geist (Wed Sep 25 2013 - 08:35:15 CDT)
Organic molecule and membrane. NAMD gives fatal error: Villalain Boullon, Jose (Wed Sep 25 2013 - 08:27:59 CDT)
- Re: Organic molecule and membrane. NAMD gives fatal error: Aron Broom (Wed Sep 25 2013 - 08:35:14 CDT)
- Re: Organic molecule and membrane. NAMD gives fatal error: Kenno Vanommeslaeghe (Wed Sep 25 2013 - 12:33:54 CDT)
pair interaction energy calculation Behnam Rasti (Wed Sep 25 2013 - 06:20:35 CDT)
Coordinates of Carbon atoms on Graphite Mihaela Drenscko (Tue Sep 24 2013 - 11:47:28 CDT)
- AW: Coordinates of Carbon atoms on Graphite Norman Geist (Wed Sep 25 2013 - 00:49:32 CDT)
cell origin problem Haleh Abdizadeh (Tue Sep 24 2013 - 09:53:17 CDT)
- AW: cell origin problem Norman Geist (Wed Sep 25 2013 - 00:44:46 CDT)
CHARMGUI and ligands parametrisation James Starlight (Tue Sep 24 2013 - 09:38:30 CDT)
- Re: CHARMGUI and ligands parametrisation Sunhwan Jo (Tue Sep 24 2013 - 10:34:40 CDT)
  - Re: CHARMGUI and ligands parametrisation James Starlight (Tue Sep 24 2013 - 15:35:09 CDT)
- Re: CHARMGUI and ligands parametrisation Kenno Vanommeslaeghe (Tue Sep 24 2013 - 10:54:37 CDT)
vibrational modes calculation Mortaza Aghtar (Mon Sep 23 2013 - 08:55:27 CDT)
How to setting tilt component in colvars module ¼¿ëÀÏ (Mon Sep 23 2013 - 01:21:35 CDT)
- Re: How to setting tilt component in colvars module Giacomo Fiorin (Mon Sep 23 2013 - 09:43:35 CDT)
  - Re: How to setting tilt component in colvars module ¼¿ëÀÏ (Mon Sep 23 2013 - 22:54:26 CDT)
Psfgen - bonding terms involving disulfide bridges Reza (Sun Sep 22 2013 - 22:26:33 CDT)
- Re: Psfgen - bonding terms involving disulfide bridges JÃ©rÃ´me HÃ©nin (Fri Oct 04 2013 - 06:55:47 CDT)
  - Re: Psfgen - bonding terms involving disulfide bridges Reza (Fri Oct 04 2013 - 09:32:46 CDT)
namd conf file oguz gurbulak (Sat Sep 21 2013 - 05:52:23 CDT)
About Muticore Linux Ibnstalltion if NAmd Vidhya Sankar (Fri Sep 20 2013 - 22:50:38 CDT)
- Re: About Muticore Linux Ibnstalltion if NAmd Aron Broom (Fri Sep 20 2013 - 23:29:04 CDT)
- Re: About Muticore Linux Ibnstalltion if NAmd Kenno Vanommeslaeghe (Tue Sep 24 2013 - 11:32:07 CDT)
FEP failure - FFTW problem? JC Gumbart (Fri Sep 20 2013 - 14:16:37 CDT)
Regarding Membrane Builder Vidhya Sankar (Fri Sep 20 2013 - 08:40:51 CDT)
(no subject) rasti_at_ut.ac.ir (Fri Sep 20 2013 - 05:19:37 CDT)
Re: About the scope of show_replicas.vmd Niklaus Johner (Thu Sep 19 2013 - 09:48:11 CDT)
- Re: About the scope of show_replicas.vmd Francesco Pietra (Thu Sep 19 2013 - 10:53:58 CDT)
  - Re: About the scope of show_replicas.vmd Jason Swails (Thu Sep 19 2013 - 11:19:24 CDT)
  - Re: About the scope of show_replicas.vmd Niklaus Johner (Thu Sep 19 2013 - 12:30:05 CDT)
    - Re: About the scope of show_replicas.vmd Francesco Pietra (Fri Sep 20 2013 - 02:33:19 CDT)
    - Re: About the scope of show_replicas.vmd Kenno Vanommeslaeghe (Fri Sep 20 2013 - 12:22:39 CDT)
- Re: About the scope of show_replicas.vmd Francesco Pietra (Fri Sep 20 2013 - 12:39:16 CDT)
  - Re: About the scope of show_replicas.vmd Kenno Vanommeslaeghe (Tue Sep 24 2013 - 11:19:21 CDT)
delta-G calculation rasti_at_ut.ac.ir (Thu Sep 19 2013 - 03:02:33 CDT)
- Re: delta-G calculation Yi Wang, PhD (Thu Sep 19 2013 - 03:08:28 CDT)
- Re: delta-G calculation Axel Kohlmeyer (Thu Sep 19 2013 - 03:09:43 CDT)
About the scope of show_replicas.vmd Francesco Pietra (Thu Sep 19 2013 - 01:48:16 CDT)
Reg Membrane Builder Vidhya Sankar (Wed Sep 18 2013 - 12:08:59 CDT)
- Re: Reg Membrane Builder Sunhwan Jo (Wed Sep 18 2013 - 12:26:06 CDT)
About Psfgen for membrane Vidhya Sankar (Wed Sep 18 2013 - 10:56:30 CDT)
Energy Correction Term For PME Electrostatics in a Charged Periodic System David Huggins (Wed Sep 18 2013 - 05:02:52 CDT)
incorrect bond Nadia Salami (Wed Sep 18 2013 - 01:28:59 CDT)
incorrect bond Nadia Salami (Wed Sep 18 2013 - 01:11:08 CDT)
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Anna Chailyan (Tue Sep 17 2013 - 11:10:29 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Niklaus Johner (Tue Sep 17 2013 - 11:35:45 CDT)
  - Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Kenno Vanommeslaeghe (Tue Sep 17 2013 - 18:20:38 CDT)
Segmentation fault - colvar Peterson J (Mon Sep 16 2013 - 23:02:55 CDT)
CHAMBER generated .prmtop file is not compatable with namd2 sudipta (Sun Sep 15 2013 - 23:51:48 CDT)
- Re: CHAMBER generated .prmtop file is not compatable with namd2 Jason Swails (Mon Sep 16 2013 - 04:55:09 CDT)
NAMD PERFORMANCE ON NVIDIA K20 GPU Neeraj Agrawal (Sat Sep 14 2013 - 18:59:08 CDT)
- Re: NAMD PERFORMANCE ON NVIDIA K20 GPU Aron Broom (Sat Sep 14 2013 - 20:19:23 CDT)
  - Re: NAMD PERFORMANCE ON NVIDIA K20 GPU Neeraj Agrawal (Tue Sep 17 2013 - 18:13:34 CDT)
- AW: NAMD PERFORMANCE ON NVIDIA K20 GPU Norman Geist (Mon Sep 16 2013 - 02:05:34 CDT)
  - Re: AW: NAMD PERFORMANCE ON NVIDIA K20 GPU Kenno Vanommeslaeghe (Tue Sep 17 2013 - 18:42:55 CDT)
Replica exchange and colvars - Missing Stage from restart Andrei Tudor (Sat Sep 14 2013 - 10:04:43 CDT)
- Re: Replica exchange and colvars - Missing Stage from restart JÃ©rÃ´me HÃ©nin (Sun Sep 15 2013 - 15:41:54 CDT)
How to optimize parameters in command for NAMD CUDA GPU MD calculations? Michael Shokhen (Thu Sep 12 2013 - 14:59:21 CDT)
- Re: How to optimize parameters in command for NAMD CUDA GPU MD calculations? Aron Broom (Thu Sep 12 2013 - 15:41:50 CDT)
Patching protein with phosphoserine, phosphothreonine and phosphotyrosine patches Rehan Zafar (Thu Sep 12 2013 - 03:41:08 CDT)
Does stray PME charges with T-REMD mean insufficient resources and can explicit water abandoned for implicit GB? Francesco Pietra (Wed Sep 11 2013 - 09:24:59 CDT)
MMPBSA calculation using NAMD sudipta (Wed Sep 11 2013 - 07:37:57 CDT)
- Re: MMPBSA calculation using NAMD Aron Broom (Sun Sep 15 2013 - 17:49:19 CDT)
Regarding the Protein-Ligand Free Energy Tutorial Aron Broom (Wed Sep 11 2013 - 00:39:18 CDT)
NAMD CUDA performance Vlastimil ZÃma (Tue Sep 10 2013 - 07:59:41 CDT)
- Re: NAMD CUDA performance Aron Broom (Tue Sep 10 2013 - 14:30:26 CDT)
  - AW: NAMD CUDA performance Norman Geist (Wed Sep 11 2013 - 01:53:54 CDT)
  - Re: NAMD CUDA performance Vlastimil ZÃma (Wed Sep 11 2013 - 04:04:08 CDT)
Stray PME grid charges on increasing number of replicas and T-range with T-REMD Francesco Pietra (Tue Sep 10 2013 - 05:24:58 CDT)
- Fwd: Stray PME grid charges on increasing number of replicas and T-range with T-REMD Francesco Pietra (Tue Sep 10 2013 - 05:33:03 CDT)
- Re: Stray PME grid charges on increasing number of replicas and T-range with T-REMD Francesco Pietra (Tue Sep 10 2013 - 11:34:58 CDT)
bilayer creation Richard Wood (Mon Sep 09 2013 - 14:00:43 CDT)
- Re: bilayer creation Axel Kohlmeyer (Mon Sep 09 2013 - 14:15:56 CDT)
  - Re: bilayer creation Richard Wood (Mon Sep 09 2013 - 14:58:39 CDT)
    - Re: bilayer creation Axel Kohlmeyer (Mon Sep 09 2013 - 15:15:24 CDT)
    - Re: bilayer creation Richard Wood (Mon Sep 09 2013 - 15:50:18 CDT)
Equilibration of the membrane bilayers with CUDA-support James Starlight (Mon Sep 09 2013 - 10:16:40 CDT)
- Re: Equilibration of the membrane bilayers with CUDA-support James Starlight (Tue Sep 10 2013 - 09:06:11 CDT)
  - Re: Equilibration of the membrane bilayers with CUDA-support Axel Kohlmeyer (Tue Sep 10 2013 - 09:14:55 CDT)
    - Re: Equilibration of the membrane bilayers with CUDA-support James Starlight (Wed Sep 11 2013 - 01:31:05 CDT)
    - Re: Equilibration of the membrane bilayers with CUDA-support Axel Kohlmeyer (Wed Sep 11 2013 - 02:14:13 CDT)
Re: explicit NVT simulation Hailey Bureau (Mon Sep 09 2013 - 08:07:19 CDT)
- Re: explicit NVT simulation Axel Kohlmeyer (Mon Sep 09 2013 - 08:17:45 CDT)
  - Re: explicit NVT simulation JÃ©rÃ´me HÃ©nin (Mon Sep 09 2013 - 08:31:03 CDT)
AW: vmd-l: Error: Maximum number of bonds exceeded Norman Geist (Mon Sep 09 2013 - 01:06:38 CDT)
explicit NVT simulation Hailey Bureau (Sun Sep 08 2013 - 17:54:26 CDT)
- AW: explicit NVT simulation Norman Geist (Mon Sep 09 2013 - 01:26:14 CDT)
About a REMD tutorial Francesco Pietra (Sat Sep 07 2013 - 09:35:51 CDT)
VDW energy is negative but total energy is positive dayanidhi mohanta (Fri Sep 06 2013 - 23:18:51 CDT)
- AW: VDW energy is negative but total energy is positive Norman Geist (Mon Sep 09 2013 - 01:14:20 CDT)
- RE: VDW energy is negative but total energy is positive Bennion, Brian (Mon Sep 09 2013 - 10:25:53 CDT)
- RE: VDW energy is negative but total energy is positive Bennion, Brian (Tue Sep 10 2013 - 10:57:23 CDT)
Atom indices in collective variable definition Randy J. Zauhar (Fri Sep 06 2013 - 09:40:09 CDT)
- Re: Atom indices in collective variable definition Aron Broom (Fri Sep 06 2013 - 09:47:30 CDT)
  - Re: Atom indices in collective variable definition JÃ©rÃ´me HÃ©nin (Fri Sep 06 2013 - 09:56:06 CDT)
charm-gui membrane builder James Starlight (Fri Sep 06 2013 - 06:21:15 CDT)
- Re: charm-gui membrane builder Sunhwan Jo (Fri Sep 06 2013 - 07:39:34 CDT)
- Re: charm-gui membrane builder James Starlight (Fri Nov 01 2013 - 04:23:07 CDT)
forward minh nhut (Thu Sep 05 2013 - 21:01:00 CDT)
- Re: forward Gianluca Interlandi (Thu Sep 05 2013 - 21:43:40 CDT)
question on explicit solvent reproducibility Hailey Bureau (Thu Sep 05 2013 - 16:31:52 CDT)
Re: parallel code in tclforce script Axel Kohlmeyer (Thu Sep 05 2013 - 02:02:36 CDT)
- Re: parallel code in tclforce script Teerapong Pirojsirikul (Thu Sep 05 2013 - 18:48:42 CDT)
  - Re: parallel code in tclforce script Axel Kohlmeyer (Fri Sep 06 2013 - 00:48:44 CDT)
AW: vmd-l: how to enable multiple core rendering? Norman Geist (Thu Sep 05 2013 - 01:01:40 CDT)
parallel code in tclforce script Teerapong Pirojsirikul (Wed Sep 04 2013 - 22:03:15 CDT)
- AW: parallel code in tclforce script Norman Geist (Thu Sep 05 2013 - 01:45:08 CDT)
Simulation of the membrane protein James Starlight (Wed Sep 04 2013 - 11:16:35 CDT)
- Re: Simulation of the membrane protein Aron Broom (Wed Sep 04 2013 - 12:26:00 CDT)
  - Re: Simulation of the membrane protein James Starlight (Thu Sep 05 2013 - 00:35:26 CDT)
Fwd: deca-alanin folding by remd parallel tempering Francesco Pietra (Wed Sep 04 2013 - 04:35:45 CDT)
namd scale-up Revthi Sanker (Wed Sep 04 2013 - 02:43:24 CDT)
- Re: namd scale-up Axel Kohlmeyer (Wed Sep 04 2013 - 03:00:30 CDT)
AW: AW: AW: pbc error Norman Geist (Tue Sep 03 2013 - 04:55:03 CDT)
pbc problem jinxj (Tue Sep 03 2013 - 04:45:06 CDT)
Error with show_replicas.vmd Francesco Pietra (Tue Sep 03 2013 - 04:44:55 CDT)
- Re: vmd-l: Error with show_replicas.vmd John Stone (Tue Sep 03 2013 - 10:57:26 CDT)
writedcd problem jinxj (Mon Sep 02 2013 - 09:32:00 CDT)
- AW: writedcd problem Norman Geist (Tue Sep 03 2013 - 03:47:16 CDT)
pbc problem jinxj (Mon Sep 02 2013 - 04:08:28 CDT)
creating coarse grain model with martini force field ¼¿ëÀÏ (Mon Sep 02 2013 - 01:58:10 CDT)
pbc error jinxj (Sun Sep 01 2013 - 21:38:48 CDT)
- AW: pbc error Norman Geist (Mon Sep 02 2013 - 01:44:18 CDT)
(no subject) Nadia Salami (Sun Sep 01 2013 - 10:26:51 CDT)
- Re: Axel Kohlmeyer (Sun Sep 01 2013 - 10:40:27 CDT)
NAMD job submission on Kraken? Martin, Erik W (Fri Aug 30 2013 - 15:36:03 CDT)
- Re: NAMD job submission on Kraken? Giacomo Fiorin (Fri Aug 30 2013 - 15:37:56 CDT)
FW: editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 13:14:33 CDT)
- Re: FW: editing the code of the non bonded pair potentials Axel Kohlmeyer (Fri Aug 30 2013 - 14:08:53 CDT)
Assigning atom serial number after the first 99999 atoms Shyno Mathew (Fri Aug 30 2013 - 11:07:49 CDT)
Margin setup Tian Li (Fri Aug 30 2013 - 08:37:03 CDT)
editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 04:27:19 CDT)
- FW: editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 04:31:44 CDT)
- Re: editing the code of the non bonded pair potentials Axel Kohlmeyer (Fri Aug 30 2013 - 04:34:46 CDT)
  - RE: editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 05:26:41 CDT)
AW: vmd-l: SangbaeLee: question about pbc wrap Norman Geist (Fri Aug 30 2013 - 02:15:30 CDT)
ABF historyFile and distFile Sridhar Kumar Kannam (Thu Aug 29 2013 - 22:58:33 CDT)
Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field sunyeping (Thu Aug 29 2013 - 21:32:22 CDT)
- Re: Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field Gianluca Interlandi (Thu Aug 29 2013 - 22:58:38 CDT)
problem in determining atom types and charges for ligand atoms to type in the topology file Mamon Hatmal (Thu Aug 29 2013 - 06:03:17 CDT)
- Re: problem in determining atom types and charges for ligand atoms to type in the topology file Kenno Vanommeslaeghe (Thu Aug 29 2013 - 09:00:58 CDT)
  - Re: problem in determining atom types and charges for ligand atoms to type in the topology file Mamon Hatmal (Thu Aug 29 2013 - 11:28:27 CDT)
how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? Ana Celia Vila Verde (Thu Aug 29 2013 - 04:07:02 CDT)
eigenvector colvar Steven Mike (Wed Aug 28 2013 - 23:14:49 CDT)
- Re: eigenvector colvar Giacomo Fiorin (Thu Aug 29 2013 - 09:00:56 CDT)
  - Re: eigenvector colvar Steven Mike (Thu Aug 29 2013 - 13:24:41 CDT)
How to prepare FEP input files for double mutant Aman (Wed Aug 28 2013 - 15:05:19 CDT)
WG: questions regarding the source code in NAMD Norman Geist (Wed Aug 28 2013 - 10:49:31 CDT)
error when doing minimization with the charmm Drude FF Frank Haverkort (Wed Aug 28 2013 - 05:23:49 CDT)
- Re: error when doing minimization with the charmm Drude FF Frank Haverkort (Fri Aug 30 2013 - 08:48:43 CDT)
LJcorrection Gianluca Interlandi (Wed Aug 28 2013 - 01:33:39 CDT)
making patch rasti_at_ut.ac.ir (Tue Aug 27 2013 - 18:41:06 CDT)
- Re: making patch Kenno Vanommeslaeghe (Tue Aug 27 2013 - 19:07:40 CDT)
- AW: making patch Norman Geist (Wed Aug 28 2013 - 02:46:00 CDT)
Linear force ramp increments in ABF Matthew Ralph Adendorff (Tue Aug 27 2013 - 12:44:41 CDT)
- Re: Linear force ramp increments in ABF JÃ©rÃ´me HÃ©nin (Thu Aug 29 2013 - 12:06:49 CDT)
  - RE: Linear force ramp increments in ABF Matthew Ralph Adendorff (Thu Aug 29 2013 - 13:40:42 CDT)
    - Re: Linear force ramp increments in ABF JÃ©rÃ´me HÃ©nin (Thu Aug 29 2013 - 14:15:43 CDT)
    - RE: Linear force ramp increments in ABF Matthew Ralph Adendorff (Thu Aug 29 2013 - 14:56:30 CDT)
excluded interactions (NNB) in psf file for FEP simulations Aman (Tue Aug 27 2013 - 10:16:38 CDT)
problem in finding atom types for ligand Mamon Hatmal (Tue Aug 27 2013 - 06:54:38 CDT)
- Re: problem in finding atom types for ligand Kenno Vanommeslaeghe (Tue Aug 27 2013 - 11:02:10 CDT)
CUDA error memcpy to exclusions: invalid argument Haleh Abdizadeh (Tue Aug 27 2013 - 04:06:29 CDT)
- Re: CUDA error memcpy to exclusions: invalid argument Axel Kohlmeyer (Tue Aug 27 2013 - 04:15:23 CDT)
  - Re: CUDA error memcpy to exclusions: invalid argument Haleh Abdizadeh (Tue Aug 27 2013 - 05:13:11 CDT)
    - Re: CUDA error memcpy to exclusions: invalid argument Axel Kohlmeyer (Tue Aug 27 2013 - 05:15:45 CDT)
problem with ptch ... rasti (Mon Aug 26 2013 - 15:21:36 CDT)
- AW: problem with ptch ... Norman Geist (Tue Aug 27 2013 - 03:40:58 CDT)
Targeted and Steered MD: Why must the initial and targeted PDBs have identical # of atoms? Bryan Roessler (Mon Aug 26 2013 - 11:24:31 CDT)
- RE: Targeted and Steered MD: Why must the initial and targeted PDBs have identical # of atoms? Tristan Croll (Tue Aug 27 2013 - 19:27:26 CDT)
Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'? Jose Borreguero (Mon Aug 26 2013 - 08:24:32 CDT)
- Re: Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'? Ajasja LjubetiÄ (Mon Aug 26 2013 - 08:49:08 CDT)
- Re: Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'? Gianluca Interlandi (Mon Aug 26 2013 - 11:56:47 CDT)
  - Re: Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'? Jose Borreguero (Tue Aug 27 2013 - 16:25:38 CDT)
AW: vmd-l: matching part of two models Norman Geist (Mon Aug 26 2013 - 04:58:04 CDT)
a problem about pbc in a namd trajectory ½ùÏþ½Ü (Mon Aug 26 2013 - 02:44:23 CDT)
- AW: a problem about pbc in a namd trajectory Norman Geist (Mon Aug 26 2013 - 03:44:14 CDT)
(no subject) kaushik chakraborty (Sun Aug 25 2013 - 11:41:34 CDT)
NAMD with pbs script k.manzoorolajdad (Sun Aug 25 2013 - 09:36:58 CDT)
- Re: NAMD with pbs script Branko (Sun Aug 25 2013 - 10:20:28 CDT)
  - Re: NAMD with pbs script k.manzoorolajdad (Tue Sep 03 2013 - 02:22:54 CDT)
problem with using patch LINK ... rasti (Sun Aug 25 2013 - 07:54:50 CDT)
- Re: problem with using patch LINK ... Victor (Sun Aug 25 2013 - 11:28:45 CDT)
problem with using patch LINK ... rasti (Sat Aug 24 2013 - 07:50:16 CDT)
Computational Biophysics Workshop using NAMD and VMD, November 18-22, 2013, Urbana, Illinois, USA David Brandon (Fri Aug 23 2013 - 14:07:30 CDT)
Implementation of ELASTIC NETWORK model in NAMD Vibhor Agrawal (Fri Aug 23 2013 - 10:57:17 CDT)
- Re: Implementation of ELASTIC NETWORK model in NAMD Victor (Fri Aug 23 2013 - 12:29:01 CDT)
obtaining cellBasisVectors from SCALE entries in the PDB file Jose Borreguero (Fri Aug 23 2013 - 10:31:28 CDT)
questions regarding the source code in NAMD Asaf Farhi (Fri Aug 23 2013 - 06:12:59 CDT)
- AW: questions regarding the source code in NAMD Norman Geist (Fri Aug 23 2013 - 06:59:34 CDT)
understanding the lone pair section of psf files Frank Haverkort (Thu Aug 22 2013 - 10:44:17 CDT)
- Re: understanding the lone pair section of psf files Hadi (Fri Aug 23 2013 - 12:11:39 CDT)
remd restart Francesco Pietra (Thu Aug 22 2013 - 06:00:40 CDT)
AW: AW: hi every body, Norman Geist (Thu Aug 22 2013 - 04:39:38 CDT)
- Re: AW: AW: hi every body, Kenno Vanommeslaeghe (Thu Aug 22 2013 - 22:30:11 CDT)
hi every body, rasti (Wed Aug 21 2013 - 17:19:05 CDT)
- AW: hi every body, Norman Geist (Thu Aug 22 2013 - 02:16:39 CDT)
Low global exclusion count on parallel tempering, not on MD Francesco Pietra (Wed Aug 21 2013 - 10:45:05 CDT)
- Fwd: Low global exclusion count on parallel tempering, not on MD Francesco Pietra (Wed Aug 21 2013 - 11:27:44 CDT)
  - Fwd: Low global exclusion count on parallel tempering, not on MD Francesco Pietra (Thu Aug 22 2013 - 03:32:18 CDT)
Defining colvars groups of atoms for ABF Maria Pikoula (Wed Aug 21 2013 - 04:13:57 CDT)
Nvidia GPUs Thomas Albers (Tue Aug 20 2013 - 13:27:28 CDT)
- Re: Nvidia GPUs Thomas C. Bishop (Tue Aug 20 2013 - 14:22:10 CDT)
  - AW: Nvidia GPUs Norman Geist (Wed Aug 21 2013 - 03:22:12 CDT)
General query re: symmetry restraints Tristan Croll (Mon Aug 19 2013 - 22:33:02 CDT)
catdcd error Revthi Sanker (Mon Aug 19 2013 - 07:15:04 CDT)
- Re: catdcd error Niklaus Johner (Mon Aug 19 2013 - 08:26:24 CDT)
- Re: catdcd error Suresh (Mon Aug 19 2013 - 08:43:35 CDT)
- AW: catdcd error Norman Geist (Mon Aug 19 2013 - 08:53:59 CDT)
apoa1 slow Phase 1 Jan Fredin (Thu Aug 15 2013 - 16:25:11 CDT)
- AW: apoa1 slow Phase 1 Norman Geist (Fri Aug 16 2013 - 00:32:09 CDT)
Normal Mode Analysis in NAMD Vibhor Agrawal (Thu Aug 15 2013 - 09:06:09 CDT)
RE: CHARMM-c36, glycans and RATTLE Tristan Croll (Thu Aug 15 2013 - 01:05:32 CDT)
- Re: CHARMM-c36, glycans and RATTLE Sunhwan Jo (Thu Aug 15 2013 - 01:09:40 CDT)
  - RE: CHARMM-c36, glycans and RATTLE Tristan Croll (Thu Aug 15 2013 - 01:23:50 CDT)
CHARMM-c36, glycans and RATTLE Tristan Croll (Wed Aug 14 2013 - 23:50:36 CDT)
Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Lucas (Wed Aug 14 2013 - 17:09:56 CDT)
- AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Norman Geist (Thu Aug 15 2013 - 00:50:54 CDT)
- Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Lucas (Thu Aug 15 2013 - 01:53:22 CDT)
  - AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Norman Geist (Thu Aug 15 2013 - 02:12:58 CDT)
- Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Paul Rigor (Thu Aug 15 2013 - 11:15:40 CDT)
- Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Lucas (Thu Aug 15 2013 - 17:26:07 CDT)
  - Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Kenno Vanommeslaeghe (Thu Aug 15 2013 - 22:25:07 CDT)
    - Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. JC Gumbart (Tue Aug 20 2013 - 13:14:27 CDT)
  - AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Norman Geist (Fri Aug 16 2013 - 00:22:44 CDT)
All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Lucas (Tue Aug 13 2013 - 13:06:06 CDT)
- AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Norman Geist (Wed Aug 14 2013 - 00:41:31 CDT)
Non-equilibrium effects in ABF runs Matthew Ralph Adendorff (Tue Aug 13 2013 - 11:38:57 CDT)
- Re: Non-equilibrium effects in ABF runs Aron Broom (Tue Aug 13 2013 - 15:59:16 CDT)
  - Re: Non-equilibrium effects in ABF runs Q=AF=9B=E8=BF=90=E9=93=96?= (Fri Aug 16 2013 - 13:28:05 CDT)
Incorporating some ions with specific location Stephan Grein (Tue Aug 13 2013 - 03:04:10 CDT)
- Re: Incorporating some ions with specific location Niklaus Johner (Tue Aug 13 2013 - 08:43:04 CDT)
unsubscribe Hamze Rahimi (Mon Aug 12 2013 - 23:37:05 CDT)
problem with restraining a dihedral angle Sijia (Scarlett) Dong (Mon Aug 12 2013 - 18:55:33 CDT)
- Re: problem with restraining a dihedral angle Victor (Tue Aug 13 2013 - 19:19:59 CDT)
unsuscribe Cat Chenal (Mon Aug 12 2013 - 10:01:42 CDT)
colvars and parallel-tempering with namd2.10 Francesco Pietra (Mon Aug 12 2013 - 09:54:25 CDT)
- Re: colvars and parallel-tempering with namd2.10 Sunhwan Jo (Mon Aug 12 2013 - 10:29:23 CDT)
  - Re: colvars and parallel-tempering with namd2.10 JÃ©rÃ´me HÃ©nin (Tue Aug 13 2013 - 09:51:30 CDT)
Re: AW: vmd-l: Occupancy maps Axel Kohlmeyer (Mon Aug 12 2013 - 01:14:52 CDT)
- AW: AW: vmd-l: Occupancy maps Norman Geist (Mon Aug 12 2013 - 01:47:30 CDT)
  - RE : AW: vmd-l: Occupancy maps Andrei Tudor (Mon Aug 12 2013 - 10:40:27 CDT)
    - AW: AW: vmd-l: Occupancy maps Norman Geist (Tue Aug 13 2013 - 03:28:25 CDT)
AW: vmd-l: Occupancy maps Norman Geist (Mon Aug 12 2013 - 00:14:36 CDT)
ERROR IN TIP4P WATER SIMULATION IN NAMD2.9 Uday Midya (Sun Aug 11 2013 - 07:09:05 CDT)
- Re:ERROR IN TIP4P WATER SIMULATION IN NAMD2.9 Roman Shirokov (Tue Sep 03 2013 - 16:44:57 CDT)
ERROR IN TIP4P WATER SIMULATION IN NAMD2.9 Uday Midya (Sun Aug 11 2013 - 02:19:47 CDT)
replica exchange parallel tempering BlueGene/Q Francesco Pietra (Sun Aug 11 2013 - 01:15:04 CDT)
- Re: replica exchange parallel tempering BlueGene/Q Francesco Pietra (Mon Aug 12 2013 - 02:25:42 CDT)
Question about loading velocity files on VMD Ganesh Kamath (Fri Aug 09 2013 - 10:01:17 CDT)
- AW: Question about loading velocity files on VMD Norman Geist (Sun Aug 11 2013 - 23:48:35 CDT)
Compile NAMD2.9 on Xeon Phi Devang Jane (Thu Aug 08 2013 - 13:15:38 CDT)
unsuscribe Cat Chenal (Thu Aug 08 2013 - 12:20:16 CDT)
NBFIX 1-4 scaling term ignored for CHARMM format parameters Sunhwan Jo (Wed Aug 07 2013 - 15:21:33 CDT)
- AW: NBFIX 1-4 scaling term ignored for CHARMM format parameters Norman Geist (Thu Aug 08 2013 - 00:27:43 CDT)
  - Re: AW: NBFIX 1-4 scaling term ignored for CHARMM format parameters Kenno Vanommeslaeghe (Thu Aug 08 2013 - 11:16:59 CDT)
AW: Colvar cannot be ran on supercomputer newton Norman Geist (Wed Aug 07 2013 - 02:18:25 CDT)
- Re: AW: Colvar cannot be ran on supercomputer newton Branko (Wed Aug 07 2013 - 03:04:23 CDT)
Evaluate energy of "protein + two closest ions" Xiaodong Pang (Tue Aug 06 2013 - 17:25:45 CDT)
Colvar cannot be ran on supercomputer newton Tian Li (Tue Aug 06 2013 - 08:35:44 CDT)
- Re: Colvar cannot be ran on supercomputer newton Ajasja LjubetiÄ (Tue Aug 06 2013 - 09:08:25 CDT)
- AW: Colvar cannot be ran on supercomputer newton Norman Geist (Tue Aug 06 2013 - 09:57:32 CDT)
  - Re: AW: Colvar cannot be ran on supercomputer newton Branko (Wed Aug 07 2013 - 11:25:38 CDT)
namd/bluegeneQ Francesco Pietra (Mon Aug 05 2013 - 12:48:07 CDT)
Special constraint on MD simulation Carlos Navarrro Retamal (Mon Aug 05 2013 - 04:13:33 CDT)
- Re: Special constraint on MD simulation JÃ©rÃ´me HÃ©nin (Mon Aug 05 2013 - 12:46:05 CDT)
Problem of ATP mutated to dATP in solution using FEP method dbaogen (Mon Aug 05 2013 - 02:14:24 CDT)
Question about converting velocities DCD to ascii plain text Joe Janicki (Sat Aug 03 2013 - 13:24:11 CDT)
- Re: Question about converting velocities DCD to ascii plain text Axel Kohlmeyer (Sat Aug 03 2013 - 14:38:36 CDT)
BKS potential nadia salami (Sat Aug 03 2013 - 12:54:40 CDT)
- Re: BKS potential Marzieh Alishahi (Sat Aug 03 2013 - 13:39:33 CDT)
Annealing of SiO nadia salami (Fri Aug 02 2013 - 23:07:58 CDT)
RMSD calculation Vibhor Agrawal (Fri Aug 02 2013 - 21:44:47 CDT)
- Re: RMSD calculation Mert Gür (Fri Aug 02 2013 - 22:22:35 CDT)
Changing NAMD XY restraint Beaven, Andrew (Fri Aug 02 2013 - 16:29:05 CDT)
- unsubscribe please! Basak Isin (Fri Aug 02 2013 - 16:35:11 CDT)
pbc wrap Tugba Nogay (Fri Aug 02 2013 - 14:52:23 CDT)
Colvars RMSD syntax with a moving reference frame Mayne, Christopher G (Fri Aug 02 2013 - 10:14:47 CDT)
- Re: Colvars RMSD syntax with a moving reference frame JÃ©rÃ´me HÃ©nin (Fri Aug 02 2013 - 10:29:12 CDT)
  - Re: Colvars RMSD syntax with a moving reference frame Giacomo Fiorin (Fri Aug 02 2013 - 13:17:49 CDT)
    - Re: Colvars RMSD syntax with a moving reference frame Mayne, Christopher G (Fri Aug 02 2013 - 16:38:21 CDT)
running namd in parallel Revthi Sanker (Thu Aug 01 2013 - 23:39:02 CDT)
- AW: running namd in parallel Norman Geist (Fri Aug 02 2013 - 03:43:52 CDT)
Help regarding PMF with SMD Katherine Parra Pulido (Thu Aug 01 2013 - 10:06:03 CDT)
setting the polarizabilities for the Drude force field Frank Haverkort (Thu Aug 01 2013 - 06:48:59 CDT)
- Re: setting the polarizabilities for the Drude force field Hadi Dinpajooh (Thu Aug 01 2013 - 13:39:42 CDT)
- Re: setting the polarizabilities for the Drude force field Kenno Vanommeslaeghe (Fri Aug 02 2013 - 11:01:26 CDT)
  - Re: setting the polarizabilities for the Drude force field Hadi (Fri Aug 02 2013 - 13:28:46 CDT)
Center of mass motion included in Temperature? Norman Geist (Thu Aug 01 2013 - 04:53:34 CDT)
- Re: Center of mass motion included in Temperature? Kenno Vanommeslaeghe (Fri Aug 02 2013 - 11:15:09 CDT)
  - Re: Center of mass motion included in Temperature? JÃ©rÃ´me HÃ©nin (Fri Aug 02 2013 - 15:24:56 CDT)
bugs in NAMD_TI script? shunzhou Wan (Wed Jul 31 2013 - 11:57:28 CDT)
replica exchange and colvars Francesco Pietra (Wed Jul 31 2013 - 02:34:05 CDT)
- Fwd: replica exchange and colvars Francesco Pietra (Wed Jul 31 2013 - 02:49:11 CDT)
Replica exchange, colvars & harmonic restraints Andrei Tudor (Mon Jul 29 2013 - 13:36:22 CDT)
- Re: Replica exchange, colvars & harmonic restraints Giacomo Fiorin (Mon Jul 29 2013 - 16:22:56 CDT)
  - AW: Replica exchange, colvars & harmonic restraints Norman Geist (Tue Jul 30 2013 - 00:38:02 CDT)
analyzing NAMD trajectory with NAMD Energy Markus Dahlgren (Mon Jul 29 2013 - 10:13:42 CDT)
- Re: analyzing NAMD trajectory with NAMD Energy Axel Kohlmeyer (Mon Jul 29 2013 - 10:31:22 CDT)
  - Re: analyzing NAMD trajectory with NAMD Energy Markus Dahlgren (Mon Jul 29 2013 - 10:40:54 CDT)
    - Re: analyzing NAMD trajectory with NAMD Energy Axel Kohlmeyer (Mon Jul 29 2013 - 10:42:44 CDT)
Reg loadtotalforces. aravind chandrasekaran (Mon Jul 29 2013 - 06:24:31 CDT)
thernodynamics integration in NAMD sunyeping_at_aliyun.com (Sat Jul 27 2013 - 11:41:09 CDT)
Water density in the solvate plugin David Cohen-Tanugi (Fri Jul 26 2013 - 10:50:20 CDT)
- Re: Water density in the solvate plugin Axel Kohlmeyer (Fri Jul 26 2013 - 10:58:57 CDT)
  - Re: Water density in the solvate plugin Kenno Vanommeslaeghe (Mon Jul 29 2013 - 10:34:11 CDT)
Re: Using negatively charged phospholipids and no neutralization, membrane expands in the xy direction ....... Villalain Boullon, Jose (Thu Jul 25 2013 - 05:52:05 CDT)
- Re: Re: Using negatively charged phospholipids and no neutralization, membrane expands in the xy direction ....... Kenno Vanommeslaeghe (Thu Jul 25 2013 - 11:12:23 CDT)
vdwForceSwitching and PME Adrian (Wed Jul 24 2013 - 22:48:20 CDT)
pmf command Pedro Swagger (Wed Jul 24 2013 - 15:30:40 CDT)
- Re: pmf command Pedro Swagger (Thu Jul 25 2013 - 12:35:00 CDT)
  - Re: pmf command Victor Ovchinnikov (Thu Jul 25 2013 - 12:56:52 CDT)
  - Re: pmf command Giacomo Fiorin (Thu Jul 25 2013 - 13:00:50 CDT)
Minimisation issue venkata agasthya (Wed Jul 24 2013 - 15:12:06 CDT)
- Re: Minimisation issue Aron Broom (Wed Jul 24 2013 - 15:25:06 CDT)
Geometric center of a residue over time Sindu (Wed Jul 24 2013 - 05:33:32 CDT)
Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... Villalain Boullon, Jose (Wed Jul 24 2013 - 03:37:20 CDT)
- Re: Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... Kenno Vanommeslaeghe (Wed Jul 24 2013 - 11:07:42 CDT)
  - Re: Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... Aron Broom (Wed Jul 24 2013 - 12:03:47 CDT)
  - Re: Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... Niklaus Johner (Wed Jul 24 2013 - 08:45:19 CDT)
vacuum minimisation-reg Revthi Sanker (Wed Jul 24 2013 - 02:37:12 CDT)
FullDirect Electrostatics Adrian (Tue Jul 23 2013 - 09:51:53 CDT)
Restart files are empy Alessandro Mascioni (Sun Jul 21 2013 - 12:24:23 CDT)
- Re: Restart files are empy Aron Broom (Mon Jul 22 2013 - 08:33:42 CDT)
FEP simulation on membrane protein Kapil jain (Sun Jul 21 2013 - 22:37:44 CDT)
CatDCD windows binaries Axel Kohlmeyer (Fri Jul 19 2013 - 04:56:00 CDT)
Unsubscribe Priyanka Purkayastha (Fri Jul 19 2013 - 01:02:33 CDT)
- Unsubscribe Basak Isin (Fri Jul 19 2013 - 12:08:45 CDT)
  - Re: Unsubscribe Giacomo Fiorin (Fri Jul 19 2013 - 13:00:04 CDT)
Unsubscribe º«À× (Thu Jul 18 2013 - 18:42:07 CDT)
Minimization/Equilibrium problem, atoms moving too fast Adrian (Thu Jul 18 2013 - 15:28:10 CDT)
- Re: Minimization/Equilibrium problem, atoms moving too fast Aron Broom (Thu Jul 18 2013 - 16:12:32 CDT)
  - RE: Minimization/Equilibrium problem, atoms moving too fast adrian palacios (Thu Jul 18 2013 - 19:58:47 CDT)
Implicit water with explicit ions Adrian (Thu Jul 18 2013 - 13:10:49 CDT)
- Unsubscribe Basak Isin (Thu Jul 18 2013 - 13:16:18 CDT)
- Re: Implicit water with explicit ions Jason Swails (Thu Jul 18 2013 - 18:30:49 CDT)
  - RE: Implicit water with explicit ions adrian palacios (Thu Jul 18 2013 - 20:02:36 CDT)
    - Re: Implicit water with explicit ions Jason Swails (Thu Jul 18 2013 - 21:09:27 CDT)
Minimisation problem venkata agasthya (Thu Jul 18 2013 - 12:42:08 CDT)
- Re: Minimisation problem Rajan Vatassery (Thu Jul 18 2013 - 13:14:40 CDT)
  - Re: Minimisation problem Aron Broom (Thu Jul 18 2013 - 13:26:52 CDT)
FW: water layer in membrane protein modeling Kong, Ren (Thu Jul 18 2013 - 09:24:06 CDT)
- Re: FW: water layer in membrane protein modeling Ajasja LjubetiÄ (Thu Jul 18 2013 - 10:00:19 CDT)
question about NVE ensamble Hasan haska (Thu Jul 18 2013 - 01:56:18 CDT)
- Re: question about NVE ensamble Axel Kohlmeyer (Thu Jul 18 2013 - 03:13:56 CDT)
  - Re: question about NVE ensamble Felipe Merino (Thu Jul 18 2013 - 10:33:23 CDT)
Preventing rotation of a protein Thomas Albers (Wed Jul 17 2013 - 21:18:16 CDT)
- Re: Preventing rotation of a protein Giacomo Fiorin (Wed Jul 17 2013 - 21:31:15 CDT)
- Re: Preventing rotation of a protein Peter Jones (Wed Jul 17 2013 - 22:06:10 CDT)
Retaining conformation Riley Workman (Wed Jul 17 2013 - 14:52:44 CDT)
- Unsubscribe Basak Isin (Wed Jul 17 2013 - 16:03:49 CDT)
  - Re: Unsubscribe Axel Kohlmeyer (Wed Jul 17 2013 - 16:09:04 CDT)
- Re: Retaining conformation JÃ©rÃ´me HÃ©nin (Thu Jul 18 2013 - 06:01:09 CDT)
  - Re: Retaining conformation Tristan Croll (Sat Jul 20 2013 - 05:15:17 CDT)
Simulation at different time-steps Mare Libero (Tue Jul 16 2013 - 22:02:58 CDT)
- Re: Simulation at different time-steps Aron Broom (Tue Jul 16 2013 - 23:47:17 CDT)
Problem regarding the big DCD file Vibhor Agrawal (Tue Jul 16 2013 - 14:07:40 CDT)
- Re: Problem regarding the big DCD file Axel Kohlmeyer (Tue Jul 16 2013 - 14:12:37 CDT)
  - Re: Problem regarding the big DCD file Vibhor Agrawal (Thu Jul 18 2013 - 11:42:23 CDT)
- Re: Problem regarding the big DCD file Atanu Maity (Fri Jul 19 2013 - 01:05:08 CDT)
- Re: Problem regarding the big DCD file Nicholas M Glykos (Sat Jul 20 2013 - 07:29:04 CDT)
run NAMD command in GPU Adrian (Tue Jul 16 2013 - 14:05:17 CDT)
- Re: run NAMD command in GPU Axel Kohlmeyer (Tue Jul 16 2013 - 14:11:35 CDT)
Convergence of Sampling and Deciding on Simulation Length Aditya Ranganathan (Tue Jul 16 2013 - 06:08:15 CDT)
- Re: Convergence of Sampling and Deciding on Simulation Length Aron Broom (Tue Jul 16 2013 - 09:59:15 CDT)
  - Re: Convergence of Sampling and Deciding on Simulation Length Nikolaos Glykos (Tue Jul 16 2013 - 12:16:12 CDT)
NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Tristan Croll (Tue Jul 16 2013 - 00:14:36 CDT)
- Re: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Vibhor Agrawal (Tue Jul 16 2013 - 00:56:33 CDT)
ERROR: Could not translate the value....into a Vector for the option 'cellOrigin' Jose Borreguero (Mon Jul 15 2013 - 16:19:31 CDT)
- Re: ERROR: Could not translate the value....into a Vector for the option 'cellOrigin' Axel Kohlmeyer (Mon Jul 15 2013 - 16:25:22 CDT)
  - Re: ERROR: Could not translate the value....into a Vector for the option 'cellOrigin' Jose Borreguero (Mon Jul 15 2013 - 16:35:08 CDT)
Resample trajectory files Vibhor Agrawal (Mon Jul 15 2013 - 15:52:58 CDT)
- Re: Resample trajectory files Ajasja LjubetiÄ (Mon Jul 15 2013 - 16:02:04 CDT)
Umbrella Sampling Replica Exchange Simulations TREIKALIS Antons (Sat Jul 13 2013 - 11:24:12 CDT)
pressure profile calculation problem P.-L. Chau (Fri Jul 12 2013 - 10:47:05 CDT)
Coarse grain parameter files JAGODINSKY, JUSTIN (Fri Jul 12 2013 - 09:47:50 CDT)
(no subject) JAGODINSKY, JUSTIN (Fri Jul 12 2013 - 09:12:51 CDT)
Free Energy using atomic coordinates as CVs Teerapong Pirojsirikul (Thu Jul 11 2013 - 17:59:31 CDT)
- Re: Free Energy using atomic coordinates as CVs JÃ©rÃ´me HÃ©nin (Fri Jul 12 2013 - 05:12:23 CDT)
dcd to pdb for trajectory analysis oguz gurbulak (Thu Jul 11 2013 - 07:40:11 CDT)
- Re: dcd to pdb for trajectory analysis Gabriel Jara (Thu Jul 11 2013 - 09:43:16 CDT)
  - Re: dcd to pdb for trajectory analysis Aron Broom (Thu Jul 11 2013 - 09:49:30 CDT)
    - Re: dcd to pdb for trajectory analysis bishop_at_latech.edu (Thu Jul 11 2013 - 13:01:33 CDT)
Re: NAMD pressureProfile command P.-L. Chau (Thu Jul 11 2013 - 04:05:45 CDT)
- Re: NAMD pressureProfile command P.-L. Chau (Fri Jul 12 2013 - 11:48:30 CDT)
  - Re: NAMD pressureProfile command MEHRAN MB (Fri Jul 12 2013 - 12:33:48 CDT)
ABF subdividing the reaction coordinate Pedro Swagger (Wed Jul 10 2013 - 16:00:37 CDT)
- Re: ABF subdividing the reaction coordinate Aron Broom (Wed Jul 10 2013 - 16:22:28 CDT)
  - Re: ABF subdividing the reaction coordinate Pedro Swagger (Wed Jul 10 2013 - 16:45:15 CDT)
local pressure profile for water liquid-vapor Mashayak, Sikandar Yusufoddin (Wed Jul 10 2013 - 10:43:21 CDT)
Regarding Production Run in NAMD amit banerjee (Wed Jul 10 2013 - 00:14:34 CDT)
use of colvars to restrain the absolute positions of all atoms in a large system Abir Ganguly (Tue Jul 09 2013 - 17:01:15 CDT)
- Re: use of colvars to restrain the absolute positions of all atoms in a large system Giacomo Fiorin (Tue Jul 09 2013 - 17:16:19 CDT)
  - Re: use of colvars to restrain the absolute positions of all atoms in a large system Abir Ganguly (Tue Jul 09 2013 - 17:35:31 CDT)
    - Re: use of colvars to restrain the absolute positions of all atoms in a large system JÃ©rÃ´me HÃ©nin (Wed Jul 10 2013 - 05:07:16 CDT)
    - Re: use of colvars to restrain the absolute positions of all atoms in a large system Abir Ganguly (Wed Jul 10 2013 - 12:11:10 CDT)
- Re: use of colvars to restrain the absolute positions of all atoms in a large system Aron Broom (Tue Jul 09 2013 - 17:18:35 CDT)
gromacs to NAMD Peterson J (Tue Jul 09 2013 - 14:55:46 CDT)
- Re: gromacs to NAMD Axel Kohlmeyer (Tue Jul 09 2013 - 15:48:45 CDT)
about interaction between protein and its image in namd simulation Liqun Zhang (Tue Jul 09 2013 - 12:16:37 CDT)
- Re: about interaction between protein and its image in namd simulation Aron Broom (Tue Jul 09 2013 - 13:10:50 CDT)
minimization does not converge Revthi Sanker (Mon Jul 08 2013 - 11:43:27 CDT)
REMD history file and question Martin, Erik W (Mon Jul 08 2013 - 10:23:00 CDT)
- Re: REMD history file and question Ivana (Mon Jul 08 2013 - 11:22:36 CDT)
Replica exchange on single physical node Francesco Pietra (Sat Jul 06 2013 - 09:19:42 CDT)
- Re: Replica exchange on single physical node Francesco Pietra (Sat Jul 06 2013 - 10:37:43 CDT)
Launching namd GPU-MPI vs GPU-binary Francesco Pietra (Sat Jul 06 2013 - 02:54:00 CDT)
Drude polarizable force field Hadi (Sat Jul 06 2013 - 02:06:15 CDT)
NAMD pressureProfile command P.-L. Chau (Thu Jul 04 2013 - 16:52:00 CDT)
pressure profile calculations P.-L. Chau (Thu Jul 04 2013 - 16:43:32 CDT)
REMD-GPU Francesco Pietra (Thu Jul 04 2013 - 02:36:59 CDT)
Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Vibhor Agrawal (Thu Jul 04 2013 - 02:31:27 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Kenno Vanommeslaeghe (Thu Jul 04 2013 - 19:49:35 CDT)
  - Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Vibhor Agrawal (Thu Jul 04 2013 - 21:28:54 CDT)
NAMD configuration file Hasan haska (Wed Jul 03 2013 - 17:12:22 CDT)
Martini 2.2 and ElNeDyn in NAMD XAvier Periole (Wed Jul 03 2013 - 12:29:16 CDT)
- Re: Martini 2.2 and ElNeDyn in NAMD XAvier Periole (Thu Jul 18 2013 - 03:30:00 CDT)
Simulation of Protein with Ions Stephan Grein (Wed Jul 03 2013 - 02:47:03 CDT)
- Re: Simulation of Protein with Ions Aron Broom (Wed Jul 03 2013 - 06:02:21 CDT)
Uncovering the Elusive HIV Capsid with Kepler GPUs Running NAMD & VMD Devang Sachdev (Tue Jul 02 2013 - 13:25:57 CDT)
Slow vacuum/GBIS simulations (time to completion keeps increasing) Ole Juul Andersen (Tue Jul 02 2013 - 12:33:45 CDT)
- Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) Aron Broom (Tue Jul 02 2013 - 12:45:17 CDT)
  - RE: Slow vacuum/GBIS simulations (time to completion keeps increasing) Ole Juul Andersen (Tue Jul 02 2013 - 12:57:14 CDT)
Restarting simulation James Starlight (Tue Jul 02 2013 - 00:45:37 CDT)
- Re: Restarting simulation MEHRAN MB (Fri Jul 05 2013 - 15:52:04 CDT)
FATAL ERROR Unknown parameter in charmm parameter file Cat Chenal (Mon Jul 01 2013 - 13:19:27 CDT)
- Re: FATAL ERROR Unknown parameter in charmm parameter file Kenno Vanommeslaeghe (Mon Jul 01 2013 - 15:07:30 CDT)
bks potential sheida bagherzadeh (Mon Jul 01 2013 - 02:15:13 CDT)
- Re: bks potential sheida bagherzadeh (Sat Jul 06 2013 - 05:00:08 CDT)
Topology and parameters for nitrate and nitrite ion amin_at_imtech.res.in (Sat Jun 29 2013 - 12:51:39 CDT)
- Re: Topology and parameters for nitrate and nitrite ion flavio seixas (Sun Jun 30 2013 - 14:02:06 CDT)
  - Re: Topology and parameters for nitrate and nitrite ion Kenno Vanommeslaeghe (Sun Jun 30 2013 - 19:17:40 CDT)
  - Re: Topology and parameters for nitrate and nitrite ion amin_at_imtech.res.in (Tue Jul 02 2013 - 09:01:19 CDT)
    - Re: Topology and parameters for nitrate and nitrite ion Kenno Vanommeslaeghe (Tue Jul 02 2013 - 09:17:32 CDT)
unsubscribe Patricia Campbell (Sat Jun 29 2013 - 00:21:31 CDT)
- Re: unsubscribe Axel Kohlmeyer (Sat Jun 29 2013 - 01:56:21 CDT)
unsubscribe Patricia Campbell (Fri Jun 28 2013 - 15:39:45 CDT)
Simulation in NPT ensemble James Starlight (Fri Jun 28 2013 - 15:28:40 CDT)
Reaction field treatment Neelanjana Sengupta (Fri Jun 28 2013 - 01:24:08 CDT)
- Re: Reaction field treatment Axel Kohlmeyer (Sat Jun 29 2013 - 08:21:54 CDT)
  - Re: Reaction field treatment Axel Kohlmeyer (Mon Jul 01 2013 - 00:25:32 CDT)
    - Re: Reaction field treatment Chris Chipot (Mon Jul 01 2013 - 14:29:56 CDT)
sn-1 tail order parameter Mihaela Drenscko (Thu Jun 27 2013 - 16:33:11 CDT)
- Re: sn-1 tail order parameter Jeffrey Potoff (Thu Jun 27 2013 - 17:01:06 CDT)
analysis of simulation output James Starlight (Thu Jun 27 2013 - 13:25:38 CDT)
Fwd: Troubles to converge while running bidirectional FEP GALLY Jose Manuel (Thu Jun 27 2013 - 02:12:24 CDT)
zinc finger with ASP FIDAN SUMBUL (Thu Jun 27 2013 - 09:47:22 CDT)
Tail order parameter Mihaela Drenscko (Wed Jun 26 2013 - 19:47:11 CDT)
- Re: Tail order parameter Jeffrey Potoff (Thu Jun 27 2013 - 11:06:22 CDT)
Problem during TMD Peterson J (Wed Jun 26 2013 - 14:59:50 CDT)
Solvent Box Jon Kusner (Wed Jun 26 2013 - 12:15:31 CDT)
- Re: Solvent Box Ivana (Wed Jun 26 2013 - 12:18:00 CDT)
  - Re: Solvent Box Vibhor Agrawal (Wed Jun 26 2013 - 12:19:54 CDT)
- Re: Solvent Box Jeffrey Potoff (Wed Jun 26 2013 - 13:10:26 CDT)
About NAMD Dennis Lam (Tue Jun 25 2013 - 11:20:15 CDT)
Simulation in Collective sub-space James Starlight (Tue Jun 25 2013 - 07:52:41 CDT)
- Re: Simulation in Collective sub-space Giacomo Fiorin (Tue Jun 25 2013 - 08:03:48 CDT)
  - Re: Simulation in Collective sub-space James Starlight (Tue Jun 25 2013 - 13:21:18 CDT)
    - Re: Simulation in Collective sub-space Giacomo Fiorin (Tue Jun 25 2013 - 16:54:04 CDT)
subscribe Axel Kohlmeyer (Mon Jun 24 2013 - 15:29:29 CDT)
unsubscribe º«À× (Mon Jun 24 2013 - 15:26:49 CDT)
NAMD exiting on startup phase Bryan Roessler (Mon Jun 24 2013 - 09:52:36 CDT)
Parameters for prosthetic groups James Starlight (Mon Jun 24 2013 - 06:56:03 CDT)
Protein-ligand simulation James Starlight (Mon Jun 24 2013 - 06:51:46 CDT)
- Re: Protein-ligand simulation Chris Chipot (Mon Jun 24 2013 - 07:02:24 CDT)
unsubscribe AYSEGUL TURUPCU (Mon Jun 24 2013 - 04:22:27 CDT)
unsubscribe arpita agarwal (Sun Jun 23 2013 - 23:12:39 CDT)
unsubscribe Hamze Rahimi (Sun Jun 23 2013 - 12:27:06 CDT)
unsubscribe Achani K. Yatawara (Sun Jun 23 2013 - 11:39:20 CDT)
- Re: unsubscribe stefano pieraccini (Tue Jun 25 2013 - 09:54:47 CDT)
unsubscribe º«À× (Sat Jun 22 2013 - 18:43:44 CDT)
Failure with compilation namd2.9-cuda_plumed1.3_recon Francesco Pietra (Sat Jun 22 2013 - 12:15:26 CDT)
- Fwd: Failure with compilation namd2.9-cuda_plumed1.3_recon Francesco Pietra (Mon Jun 24 2013 - 04:48:24 CDT)
unsubscribe Aysegul Turupcu (Sat Jun 22 2013 - 11:07:04 CDT)
Atom numbering Felipe Merino (Sat Jun 22 2013 - 05:34:53 CDT)
- Re: Atom numbering Giacomo Fiorin (Sat Jun 22 2013 - 10:41:35 CDT)
About Fiorin-Klein-Henin recent colvar examples Francesco Pietra (Fri Jun 21 2013 - 03:50:35 CDT)
- Re: About Fiorin-Klein-Henin recent colvar examples Giacomo Fiorin (Fri Jun 21 2013 - 09:59:06 CDT)
Insertion of GPCR in the POPC Bilayer Vibhor Agrawal (Thu Jun 20 2013 - 15:29:20 CDT)
- Re: Insertion of GPCR in the POPC Bilayer Aron Broom (Thu Jun 20 2013 - 16:27:25 CDT)
  - Re: Insertion of GPCR in the POPC Bilayer Jeffrey Potoff (Thu Jun 20 2013 - 20:12:27 CDT)
- Re: Insertion of GPCR in the POPC Bilayer Yi Wang, PhD (Thu Jun 20 2013 - 21:09:03 CDT)
- Re: Insertion of GPCR in the POPC Bilayer Ramin Ekhteiari (Fri Jun 21 2013 - 03:17:13 CDT)
  - Re: Insertion of GPCR in the POPC Bilayer Vibhor Agrawal (Fri Jun 21 2013 - 11:34:22 CDT)
Free Energy Calculation Question Kasra Fattah (Thu Jun 20 2013 - 15:28:28 CDT)
- Re: Free Energy Calculation Question Aron Broom (Thu Jun 20 2013 - 16:22:34 CDT)
- Re: Free Energy Calculation Question JÃ©rÃ´me HÃ©nin (Thu Jun 20 2013 - 16:18:57 CDT)
(no subject) Mihaela Drenscko (Thu Jun 20 2013 - 10:14:07 CDT)
- Re: Aron Broom (Thu Jun 20 2013 - 10:19:40 CDT)
  - AW: Norman Geist (Fri Jun 21 2013 - 03:11:07 CDT)
Re: C++ API Aron Broom (Thu Jun 20 2013 - 01:12:19 CDT)
Using CosntantArea in membrane simulation Peterson J (Wed Jun 19 2013 - 16:53:06 CDT)
C++ API Stephan Grein (Wed Jun 19 2013 - 08:20:11 CDT)
- AW: C++ API Norman Geist (Thu Jun 20 2013 - 01:01:53 CDT)
Basic question about impropers Wenhao Liu (Tue Jun 18 2013 - 18:30:12 CDT)
- Re: Basic question about impropers Victor (Wed Jun 19 2013 - 11:29:11 CDT)
utilizing mic coprocs on Stampede Edward Lyman (Tue Jun 18 2013 - 14:46:47 CDT)
collective variables new paper Giacomo Fiorin (Mon Jun 17 2013 - 17:48:11 CDT)
unsubscribe from mailing list Maria Kopp (Mon Jun 17 2013 - 10:24:13 CDT)
Overestimated PMF Felipe Merino (Mon Jun 17 2013 - 09:43:07 CDT)
- Re: Overestimated PMF Giacomo Fiorin (Mon Jun 17 2013 - 10:10:10 CDT)
  - Re: Overestimated PMF Felipe Merino (Mon Jun 17 2013 - 10:15:07 CDT)
- Re: Overestimated PMF JC Gumbart (Mon Jun 17 2013 - 11:37:10 CDT)
namdenergy and namd Dr. Eddie (Mon Jun 17 2013 - 08:43:44 CDT)
About Namd Installation Vidhya Sankar (Sun Jun 16 2013 - 00:14:04 CDT)
- Re: About Namd Installation Axel Kohlmeyer (Sun Jun 16 2013 - 01:23:15 CDT)
Error in PSF gen Vibhor Agrawal (Sat Jun 15 2013 - 21:18:13 CDT)
- Fwd: Error in PSF gen Vibhor Agrawal (Mon Jun 17 2013 - 11:48:27 CDT)
  - Re: Error in PSF gen Ivana (Mon Jun 17 2013 - 14:39:00 CDT)
    - Re: Error in PSF gen Vibhor Agrawal (Tue Jun 18 2013 - 22:36:32 CDT)
    - Re: Error in PSF gen Ivana (Wed Jun 19 2013 - 10:14:36 CDT)
query on constraintScaling in NAMD Peterson J (Fri Jun 14 2013 - 15:47:25 CDT)
Lipid bilayer tears apart during simulation Peterson J (Fri Jun 14 2013 - 15:14:02 CDT)
- Re: Lipid bilayer tears apart during simulation Aron Broom (Fri Jun 14 2013 - 15:34:31 CDT)
  - Re: Lipid bilayer tears apart during simulation Peterson J (Fri Jun 14 2013 - 15:44:46 CDT)
- Re: Lipid bilayer tears apart during simulation Jeffrey Potoff (Fri Jun 14 2013 - 15:46:10 CDT)
how to apply force SMD method on an anisotropic geometry Anurag Sharma (Wed Jun 12 2013 - 15:39:34 CDT)
- AW: how to apply force SMD method on an anisotropic geometry Norman Geist (Thu Jun 13 2013 - 01:56:48 CDT)
  - Re: AW: how to apply force SMD method on an anisotropic geometry JÃ©rÃ´me HÃ©nin (Thu Jun 13 2013 - 02:54:42 CDT)
    - RE: AW: how to apply force SMD method on an anisotropic geometry Anurag Sharma (Thu Jun 13 2013 - 09:41:24 CDT)
    - RE: AW: how to apply force SMD method on an anisotropic geometry Anurag Sharma (Fri Jun 21 2013 - 20:38:47 CDT)
  - RE: how to apply force SMD method on an anisotropic geometry Anurag Sharma (Fri Jun 21 2013 - 20:47:47 CDT)
FATAL ERROR: Bad global bond count! Peterson J (Wed Jun 12 2013 - 11:01:23 CDT)
Error while running the infiniband version. Shubhra Ghosh Dastidar (Wed Jun 12 2013 - 07:52:36 CDT)
How to remove center of mass translation of macromolecule Teerapong Pirojsirikul (Wed Jun 12 2013 - 03:05:36 CDT)
- Re: How to remove center of mass translation of macromolecule JÃ©rÃ´me HÃ©nin (Wed Jun 12 2013 - 04:00:48 CDT)
  - Re: How to remove center of mass translation of macromolecule Teerapong Pirojsirikul (Thu Jun 13 2013 - 17:38:07 CDT)
2014 Biophysics Workshop In Aspen Colorado MARK PLUMMER (Tue Jun 11 2013 - 20:39:57 CDT)
Workshop on GPU Programming for Molecular Modeling, August 2-4, 2013, in Urbana, Illinois David Brandon (Tue Jun 11 2013 - 17:41:43 CDT)
Re: Nonstandard ligand-DNA system Saaz Sakrikar (Tue Jun 11 2013 - 16:47:13 CDT)
abf_integrate Kasra Fattah (Tue Jun 11 2013 - 14:54:34 CDT)
- Re: abf_integrate Giacomo Fiorin (Tue Jun 11 2013 - 15:03:29 CDT)
multiple vectors in SMD yp sun (Mon Jun 10 2013 - 22:35:50 CDT)
- Re: multiple vectors in SMD JÃ©rÃ´me HÃ©nin (Thu Jun 13 2013 - 02:56:44 CDT)
Two dimensional ABF Nadeem A. Vellore (Tue Jun 11 2013 - 11:33:02 CDT)
- Re: Two dimensional ABF Branko (Tue Jun 11 2013 - 12:38:19 CDT)
- Re: Two dimensional ABF JÃ©rÃ´me HÃ©nin (Tue Jun 11 2013 - 12:35:52 CDT)
Re: NAMD related Anilkumar Naik (Tue Jun 11 2013 - 00:16:33 CDT)
- Re: NAMD related Anilkumar Naik (Tue Jun 11 2013 - 01:43:30 CDT)
  - Re: NAMD related Anilkumar Naik (Tue Jun 11 2013 - 02:14:17 CDT)
protein schematic representaton francesco oteri (Mon Jun 10 2013 - 13:23:17 CDT)
ABF simulations with barriers (adsorption) Zachary Ulissi (Mon Jun 10 2013 - 12:26:49 CDT)
- Re: ABF simulations with barriers (adsorption) JÃ©rÃ´me HÃ©nin (Tue Jun 11 2013 - 07:09:06 CDT)
  - Re: ABF simulations with barriers (adsorption) JÃ©rÃ´me HÃ©nin (Thu Jun 13 2013 - 04:45:19 CDT)
NAMD related Anilkumar Naik (Mon Jun 10 2013 - 06:35:27 CDT)
- AW: NAMD related Norman Geist (Mon Jun 10 2013 - 10:24:11 CDT)
PSF files and long atom name Reza (Sun Jun 09 2013 - 14:40:17 CDT)
- Re: PSF files and long atom name Reza (Mon Jun 10 2013 - 19:45:48 CDT)
DCD writing error on cluster Rehan Zafar (Sun Jun 09 2013 - 14:01:44 CDT)
- AW: DCD writing error on cluster Norman Geist (Mon Jun 10 2013 - 00:48:28 CDT)
Shift (or offset) of the lipid bilayer along Z axis during equilibration ç¿æž—å²½ (Fri Jun 07 2013 - 20:36:44 CDT)
- Re: Shift (or offset) of the lipid bilayer along Z axis during equilibration Aron Broom (Fri Jun 07 2013 - 20:56:46 CDT)
  - å›žå¤ï¼š Shift (or offset) of the lipid bilayer along Z axis during equilibration ç¿æž—å²½ (Fri Jun 07 2013 - 21:30:12 CDT)
    - AW: å›žå¤ï¼š Shift (or offset) of the lipid bilayer along Z axis during equilibration Norman Geist (Mon Jun 10 2013 - 00:42:35 CDT)
Problem regarding the psfgen Vibhor Agrawal (Fri Jun 07 2013 - 14:55:28 CDT)
- Re: Problem regarding the psfgen Jack Bulat (Fri Jun 07 2013 - 15:02:58 CDT)
  - Re: Problem regarding the psfgen Vibhor Agrawal (Fri Jun 07 2013 - 15:33:38 CDT)
ABF with the RMSD colvar George Patargias (Fri Jun 07 2013 - 08:51:22 CDT)
- Re: ABF with the RMSD colvar JÃ©rÃ´me HÃ©nin (Fri Jun 07 2013 - 09:07:57 CDT)
  - Re: ABF with the RMSD colvar George Patargias (Fri Jun 07 2013 - 09:43:45 CDT)
    - Re: ABF with the RMSD colvar Aron Broom (Fri Jun 07 2013 - 09:50:12 CDT)
Nucleic acid-small molecule system Saaz Sakrikar (Fri Jun 07 2013 - 01:45:49 CDT)
Fwd: NAMD tcouple atoms moving too fast Tao Qu (Thu Jun 06 2013 - 15:04:56 CDT)
Any alternative to colvars for minimization? Francesco Pietra (Thu Jun 06 2013 - 01:36:40 CDT)
- AW: Any alternative to colvars for minimization? Norman Geist (Thu Jun 06 2013 - 02:27:26 CDT)
  - Re: AW: Any alternative to colvars for minimization? JÃ©rÃ´me HÃ©nin (Thu Jun 06 2013 - 05:07:25 CDT)
- Re: Any alternative to colvars for minimization? Giacomo Fiorin (Thu Jun 06 2013 - 08:25:34 CDT)
What does "outputSystemForce" output? Ivan Mikhaylov (Wed Jun 05 2013 - 16:28:48 CDT)
- Re: What does "outputSystemForce" output? Giacomo Fiorin (Wed Jun 05 2013 - 16:49:20 CDT)
  - Re: What does "outputSystemForce" output? Ivan Mikhaylov (Wed Jun 05 2013 - 17:14:50 CDT)
    - Re: What does "outputSystemForce" output? Giacomo Fiorin (Wed Jun 05 2013 - 17:17:04 CDT)
how to do a vacuum minimization without electrostatics and periodic boundary conditions? Jose Borreguero (Wed Jun 05 2013 - 10:20:27 CDT)
- Re: how to do a vacuum minimization without electrostatics and periodic boundary conditions? Aron Broom (Wed Jun 05 2013 - 10:47:48 CDT)
  - AW: how to do a vacuum minimization without electrostatics and periodic boundary conditions? Norman Geist (Thu Jun 06 2013 - 02:12:01 CDT)
ABF zCoord analog in colvars ? Arturas (Wed Jun 05 2013 - 08:41:15 CDT)
- Re: ABF zCoord analog in colvars ? JÃ©rÃ´me HÃ©nin (Wed Jun 05 2013 - 08:44:16 CDT)
Re: fixed atom/Constraint failure in RATTLE algorithm/ MEHRAN MB (Tue Jun 04 2013 - 10:26:47 CDT)
First meeting with NAMD James Starlight (Tue Jun 04 2013 - 09:46:54 CDT)
- Re: First meeting with NAMD Giacomo Fiorin (Tue Jun 04 2013 - 10:05:52 CDT)
  - Re: First meeting with NAMD James Starlight (Wed Jun 05 2013 - 05:22:28 CDT)
    - AW: First meeting with NAMD Norman Geist (Thu Jun 06 2013 - 02:23:05 CDT)
AW: fixed atom/Constraint failure in RATTLE algorithm/ Norman Geist (Tue Jun 04 2013 - 02:01:10 CDT)
First meeting with NAMD James Starlight (Mon Jun 03 2013 - 09:08:58 CDT)
- Re: First meeting with NAMD Giacomo Fiorin (Mon Jun 03 2013 - 09:16:05 CDT)
- AW: First meeting with NAMD Norman Geist (Tue Jun 04 2013 - 02:16:18 CDT)
Invitation to connect on LinkedIn Gabriel Jara (Mon Jun 03 2013 - 08:46:22 CDT)
Does MOLLY really retain bond motion for water? Francesco Pietra (Sun Jun 02 2013 - 08:45:04 CDT)
- AW: Does MOLLY really retain bond motion for water? Norman Geist (Mon Jun 03 2013 - 00:43:15 CDT)
fixed atom/Constraint failure in RATTLE algorithm/ MEHRAN MB (Fri May 31 2013 - 11:33:03 CDT)
- AW: fixed atom/Constraint failure in RATTLE algorithm/ Norman Geist (Mon Jun 03 2013 - 00:23:43 CDT)
Fwd: Pressure in NPT ensamble Cobalto Tetracloruro (Fri May 31 2013 - 11:15:49 CDT)
A fancy problem in calculating the protonated glutamic acid modelled by adding the patch of GLUP Yize Hu (Fri May 31 2013 - 10:20:52 CDT)
- Re: A fancy problem in calculating the protonated glutamic acid modelled by adding the patch of GLUP JÃ©rÃ´me HÃ©nin (Fri May 31 2013 - 10:30:01 CDT)
  - Re: A fancy problem in calculating the protonated glutamic acid modelled by adding the patch of GLUP Yize Hu (Sat Jun 01 2013 - 03:17:27 CDT)
QM-MM Francesco Pietra (Fri May 31 2013 - 01:47:47 CDT)
AW: NAMD/VMD installation on Linux Clusters with InfiniBand Norman Geist (Thu May 30 2013 - 05:14:55 CDT)
Re: problem with runiing namd through infiniband Shubhra Ghosh Dastidar (Wed May 29 2013 - 05:13:10 CDT)
- Re: problem with runiing namd through infiniband Shubhra Ghosh Dastidar (Wed May 29 2013 - 07:41:47 CDT)
  - AW: problem with runiing namd through infiniband Norman Geist (Thu May 30 2013 - 05:05:59 CDT)
- Re: problem with runiing namd through infiniband Shubhra Ghosh Dastidar (Thu May 30 2013 - 05:15:40 CDT)
  - AW: problem with runiing namd through infiniband Norman Geist (Fri May 31 2013 - 01:04:09 CDT)
Re: namd with ff99sb Francesco Pietra (Wed May 29 2013 - 01:27:32 CDT)
Flags for TIP3 water with NAMD/AMBER FF Francesco Pietra (Tue May 28 2013 - 10:46:01 CDT)
problem with runiing namd through infiniband Shubhra Ghosh Dastidar (Tue May 28 2013 - 02:15:15 CDT)
- AW: problem with runiing namd through infiniband Norman Geist (Wed May 29 2013 - 00:22:58 CDT)
Free energy calculations karthik kumar (Mon May 27 2013 - 07:47:33 CDT)
- Re: Free energy calculations JÃ©rÃ´me HÃ©nin (Tue May 28 2013 - 05:36:55 CDT)
Suggestions while building a GPU-machine (CUDA) for NAMD use! Aditya Ranganathan (Mon May 27 2013 - 03:14:33 CDT)
- Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Axel Kohlmeyer (Mon May 27 2013 - 03:57:15 CDT)
  - Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Aditya Ranganathan (Mon May 27 2013 - 04:35:32 CDT)
    - Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Axel Kohlmeyer (Mon May 27 2013 - 04:58:05 CDT)
    - Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Aron Broom (Mon May 27 2013 - 08:09:44 CDT)
  - Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Francesco Pietra (Tue May 28 2013 - 00:55:38 CDT)
Should I use a precompiled binary? Andrew DeYoung (Fri May 24 2013 - 15:36:41 CDT)
- RE: Should I use a precompiled binary? Bennion, Brian (Fri May 24 2013 - 15:45:02 CDT)
2014 Aspen Center for Physics Workshop MARK PLUMMER (Fri May 24 2013 - 14:50:54 CDT)
Re: NAMD/VMD installation on Linux Clusters with InfiniBand Anilkumar Naik (Fri May 24 2013 - 04:55:02 CDT)
- Re: NAMD/VMD installation on Linux Clusters with InfiniBand Anilkumar Naik (Fri May 24 2013 - 08:25:10 CDT)
  - Re: NAMD/VMD installation on Linux Clusters with InfiniBand Axel Kohlmeyer (Fri May 24 2013 - 08:55:42 CDT)
    - Re: NAMD/VMD installation on Linux Clusters with InfiniBand Anilkumar Naik (Sun May 26 2013 - 00:46:47 CDT)
    - Re: NAMD/VMD installation on Linux Clusters with InfiniBand Axel Kohlmeyer (Sun May 26 2013 - 02:08:46 CDT)
- Re: NAMD/VMD installation on Linux Clusters with InfiniBand Axel Kohlmeyer (Fri May 24 2013 - 22:42:08 CDT)
  - Re: NAMD/VMD installation on Linux Clusters with InfiniBand Andrew Emerson (Mon May 27 2013 - 07:25:19 CDT)
NAMD/VMD installation on Linux Clusters with InfiniBand Anilkumar Naik (Fri May 24 2013 - 08:31:09 CDT)
Aron Broom on NVIDIA CUDA Spotlight Devang Sachdev (Wed May 22 2013 - 19:59:11 CDT)
NAMD/VMD installation on Linux Clusters with InfiniBand Anilkumar Naik (Wed May 22 2013 - 11:18:22 CDT)
- AW: NAMD/VMD installation on Linux Clusters with InfiniBand Norman Geist (Thu May 23 2013 - 01:24:51 CDT)
pressure profile freezing Thomas Brian (Wed May 22 2013 - 11:57:59 CDT)
- Re: pressure profile freezing Thomas Brian (Wed May 22 2013 - 12:41:52 CDT)
modeling missing loops in starting structures Martin, Erik W (Tue May 21 2013 - 17:08:06 CDT)
- Re: modeling missing loops in starting structures Thomas Evangelidis (Tue May 21 2013 - 17:12:44 CDT)
Molecular Shape Searching on GPUs MARK (Mon May 20 2013 - 13:13:55 CDT)
Suggestions on parameterizing a ligand to simulate in NAMD Peterson J (Mon May 20 2013 - 13:03:57 CDT)
- Re: Suggestions on parameterizing a ligand to simulate in NAMD Aron Broom (Mon May 20 2013 - 14:10:21 CDT)
- Re: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD Jiawei Xu (Mon May 20 2013 - 14:11:50 CDT)
- Re: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD Mayne, Christopher G (Mon May 20 2013 - 14:32:42 CDT)
  - Re: Re: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD Peterson J (Mon May 20 2013 - 23:48:48 CDT)
Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Corey Fugate (Mon May 20 2013 - 11:08:07 CDT)
- Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Aron Broom (Mon May 20 2013 - 11:16:35 CDT)
  - Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Corey Fugate (Mon May 20 2013 - 11:57:14 CDT)
Protein unfolding and Coarse grained Fugui (Fri May 17 2013 - 06:55:02 CDT)
- AW: Protein unfolding and Coarse grained Norman Geist (Fri May 17 2013 - 07:41:17 CDT)
- Re: Protein unfolding and Coarse grained Aron Broom (Fri May 17 2013 - 07:44:38 CDT)
Building crystal polymer Shaikh Abdul Rajjak (Fri May 17 2013 - 00:59:09 CDT)
- AW: Building crystal polymer Norman Geist (Fri May 17 2013 - 07:39:30 CDT)
Linuxtag Gianluca Interlandi (Thu May 16 2013 - 14:38:40 CDT)
Potential of mean force calculation using colvars in NADM 2.9 package ¼¿ëÀÏ (Thu May 16 2013 - 02:06:53 CDT)
- Re: Potential of mean force calculation using colvars in NADM 2.9 package Aron Broom (Thu May 16 2013 - 07:55:46 CDT)
  - Re: Potential of mean force calculation using colvars in NADM 2.9 package JÃ©rÃ´me HÃ©nin (Fri May 17 2013 - 09:21:24 CDT)
    - Re: Potential of mean force calculation using colvars in NADM 2.9 package Ajasja LjubetiÄ (Fri May 17 2013 - 09:41:40 CDT)
    - Re: Potential of mean force calculation using colvars in NADM 2.9 package JÃ©rÃ´me HÃ©nin (Fri May 17 2013 - 09:56:36 CDT)
- Re: Potential of mean force calculation using colvars in NADM 2.9 package JÃ©rÃ´me HÃ©nin (Thu May 16 2013 - 08:19:57 CDT)
A larger protein data bank for performance benchmark linux freaker (Mon May 13 2013 - 11:49:10 CDT)
- Re: A larger protein data bank for performance benchmark Cesar Millan (Mon May 13 2013 - 11:52:30 CDT)
  - Re: A larger protein data bank for performance benchmark Ajasja LjubetiÄ (Mon May 13 2013 - 12:13:46 CDT)
  - Re: A larger protein data bank for performance benchmark linux freaker (Mon May 13 2013 - 19:51:51 CDT)
Re: NAMD Tutorial - Water Sphere - Altering size of water sphere Peter Murphy (Mon May 13 2013 - 11:16:20 CDT)
Coarse-grained reverse transformation Fugui (Sat May 11 2013 - 10:21:04 CDT)
- AW: Coarse-grained reverse transformation Norman Geist (Mon May 13 2013 - 00:43:00 CDT)
Can I define a simulation box but turn off the PBC at the same time? ÕÔÀöÄÈ (Thu May 09 2013 - 03:49:48 CDT)
- AW: Can I define a simulation box but turn off the PBC at the same time? Norman Geist (Mon May 13 2013 - 00:22:55 CDT)
  - Re: AW: Can I define a simulation box but turn off the PBC at the same time? JÃ©rÃ´me HÃ©nin (Mon May 13 2013 - 03:17:29 CDT)
restart files not written. Yarrow Madrona (Thu May 09 2013 - 19:25:57 CDT)
- Re: restart files not written. Aron Broom (Thu May 09 2013 - 20:52:19 CDT)
  - Re: restart files not written. Yarrow Madrona (Fri May 10 2013 - 14:11:00 CDT)
ABF karthik kumar (Wed May 08 2013 - 23:34:17 CDT)
- Re: ABF Chris Chipot (Thu May 09 2013 - 01:09:27 CDT)
Bulk properties of polymers Sindu (Tue May 07 2013 - 23:34:20 CDT)
- AW: Bulk properties of polymers Norman Geist (Wed May 08 2013 - 02:13:56 CDT)
  - Re: AW: Bulk properties of polymers Sindu (Wed May 08 2013 - 02:33:18 CDT)
    - Re: AW: Bulk properties of polymers Axel Kohlmeyer (Wed May 08 2013 - 03:39:25 CDT)
    - Re: AW: Bulk properties of polymers Sindu (Wed May 08 2013 - 03:46:35 CDT)
- Re: Bulk properties of polymers Axel Kohlmeyer (Wed May 08 2013 - 02:28:50 CDT)
  - Re: Bulk properties of polymers Sindu (Wed May 08 2013 - 03:33:15 CDT)
fail to guess missing coordinates Liqi Feng (Tue May 07 2013 - 13:30:21 CDT)
AW: Exploding vdW energies in automatically generated POPC membranes Norman Geist (Tue May 07 2013 - 00:17:36 CDT)
BAR-estimator error of ParseFEP plugin version 1.5 in VMD 1.9.1 dbaogen (Tue May 07 2013 - 00:10:40 CDT)
- Re: BAR-estimator error of ParseFEP plugin version 1.5 in VMD 1.9.1 Chris Chipot (Tue May 07 2013 - 00:44:08 CDT)
catdcd output and .psf file atom count mismatch Izhar Karbat (Mon May 06 2013 - 17:18:53 CDT)
- AW: catdcd output and .psf file atom count mismatch Norman Geist (Tue May 07 2013 - 00:47:33 CDT)
Exploding vdW energies in automatically generated POPC membranes Lucas (Mon May 06 2013 - 15:33:47 CDT)
- AW: Exploding vdW energies in automatically generated POPC membranes Norman Geist (Tue May 07 2013 - 00:16:20 CDT)
Bad global bond count Fugui (Mon May 06 2013 - 15:26:52 CDT)
How to converse Coarse-Grained structure into all-atom structure Fugui (Mon May 06 2013 - 05:02:10 CDT)
- Re: How to converse Coarse-Grained structure into all-atom structure Axel Kohlmeyer (Mon May 06 2013 - 05:09:01 CDT)
Selecting GPU for namd2 Francesco Pietra (Mon May 06 2013 - 02:27:57 CDT)
AW: AW: Coarse-Grained fatal error! Norman Geist (Mon May 06 2013 - 01:09:08 CDT)
How to use ParseFEP plugin to carry out FEP analysis for several forward and backward *.fepout files when lambda is from 0 to 1 dbaogen (Sat May 04 2013 - 02:23:19 CDT)
- Re: How to use ParseFEP plugin to carry out FEP analysis for several forward and backward *.fepout files when lambda is from 0 to 1 Chris Chipot (Sun May 05 2013 - 02:44:48 CDT)
Sevoflurane parameters (psf file) Mikhail Suyetin (Fri May 03 2013 - 09:41:19 CDT)
- Re: Sevoflurane parameters (psf file) Branko (Fri May 03 2013 - 13:14:27 CDT)
  - Re: Sevoflurane parameters (psf file) Mikhail Suyetin (Fri May 03 2013 - 15:07:00 CDT)
    - Re: Sevoflurane parameters (psf file) JÃ©rÃ´me HÃ©nin (Mon May 06 2013 - 03:42:42 CDT)
    - Re: Sevoflurane parameters (psf file) Mikhail Suyetin (Mon May 06 2013 - 13:25:38 CDT)
unsubscribe Patricia Campbell (Fri May 03 2013 - 08:57:21 CDT)
Patching N- and C-Terms and their parameters Peterson J (Thu May 02 2013 - 18:28:25 CDT)
MDFF force threshold Ivana (Thu May 02 2013 - 10:07:17 CDT)
dihedral parameter conversion JC Gumbart (Thu May 02 2013 - 08:17:00 CDT)
- Re: dihedral parameter conversion Markus Dahlgren (Thu May 02 2013 - 09:16:36 CDT)
  - RE: dihedral parameter conversion JC Gumbart (Thu May 02 2013 - 09:41:30 CDT)
    - Re: dihedral parameter conversion Markus Dahlgren (Thu May 02 2013 - 10:08:51 CDT)
  - Re: dihedral parameter conversion JC Gumbart (Fri May 03 2013 - 00:21:10 CDT)
Coarse-Grained fatal error! Fugui (Thu May 02 2013 - 07:49:20 CDT)
- AW: Coarse-Grained fatal error! Norman Geist (Fri May 03 2013 - 00:25:54 CDT)
Current bias values Siri Søndergaard (Wed May 01 2013 - 20:39:50 CDT)
- Re: Current bias values Ajasja LjubetiÄ (Wed May 08 2013 - 02:54:11 CDT)
NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's. Aaron Cann (Tue Apr 30 2013 - 21:17:02 CDT)
- Re: NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's. Aron Broom (Tue Apr 30 2013 - 23:59:32 CDT)
  - AW: NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's. Norman Geist (Thu May 02 2013 - 01:13:08 CDT)
negative VdW energy and Elect energy ç¿æž—å²½ (Tue Apr 30 2013 - 20:50:17 CDT)
[SOLVED] Charmrun> error x attaching to node Norman Geist (Tue Apr 30 2013 - 05:09:05 CDT)
- AW: [SOLVED] Charmrun> error x attaching to node Norman Geist (Tue Apr 30 2013 - 07:09:22 CDT)
WHAM analysis for Umbrella sampling Ada Zhan (Mon Apr 29 2013 - 14:41:37 CDT)
- Re: WHAM analysis for Umbrella sampling Aron Broom (Mon Apr 29 2013 - 15:17:00 CDT)
  - Re: WHAM analysis for Umbrella sampling JÃ©rÃ´me HÃ©nin (Tue Apr 30 2013 - 04:07:52 CDT)
Fe-N bond parameters Francesco Pietra (Sun Apr 28 2013 - 09:55:16 CDT)
unrecognizable code in the output file of ParseFEP analysis in VMD 1.9.1 under the Linux system dbaogen (Sun Apr 28 2013 - 03:11:52 CDT)
Conceptual questions about GPU acceleration Andrew DeYoung (Sat Apr 27 2013 - 11:46:49 CDT)
- Re: Conceptual questions about GPU acceleration Axel Kohlmeyer (Sat Apr 27 2013 - 12:20:06 CDT)
Free energy calculation of proton transfer with FEP Huihui Liu (Sat Apr 27 2013 - 03:49:10 CDT)
Are random forces applied at every step (when using the langevin thermostat) ? Ajasja LjubetiÄ (Fri Apr 26 2013 - 15:21:56 CDT)
- AW: Are random forces applied at every step (when using the langevin thermostat) ? Norman Geist (Mon Apr 29 2013 - 01:55:37 CDT)
- Re: Are random forces applied at every step (when using the langevin thermostat) ? JÃ©rÃ´me HÃ©nin (Mon Apr 29 2013 - 03:58:22 CDT)
  - Re: Are random forces applied at every step (when using the langevin thermostat) ? Ajasja LjubetiÄ (Tue Apr 30 2013 - 10:48:46 CDT)
metadynamics Francesco Pietra (Fri Apr 26 2013 - 09:46:12 CDT)
- Re: metadynamics Axel Kohlmeyer (Fri Apr 26 2013 - 09:53:41 CDT)
  - Re: metadynamics Niklaus Johner (Fri Apr 26 2013 - 10:17:00 CDT)
    - Re: metadynamics Francesco Pietra (Fri Apr 26 2013 - 10:58:40 CDT)
  - Re: metadynamics Aron Broom (Fri Apr 26 2013 - 10:19:40 CDT)
    - Re: metadynamics Francesco Pietra (Fri Apr 26 2013 - 11:02:19 CDT)
Build polymer from monomer Sindu (Thu Apr 25 2013 - 23:48:17 CDT)
- AW: Build polymer from monomer Norman Geist (Fri Apr 26 2013 - 01:07:13 CDT)
  - Re: AW: Build polymer from monomer Sindu (Fri Apr 26 2013 - 01:22:46 CDT)
(no subject) Ganesh Shahane (Thu Apr 25 2013 - 08:51:59 CDT)
- Re: Aron Broom (Thu Apr 25 2013 - 09:34:41 CDT)
(no subject) Ganesh Shahane (Thu Apr 25 2013 - 01:25:29 CDT)
Fwd: vmd-l: HEME acting unplanar Francesco Pietra (Wed Apr 24 2013 - 15:07:54 CDT)
AW: Link between simulations Norman Geist (Wed Apr 24 2013 - 02:09:13 CDT)
binding free energy calculation yp sun (Sun Apr 21 2013 - 07:42:52 CDT)
- Re: binding free energy calculation Aron Broom (Mon Apr 22 2013 - 10:12:45 CDT)
solvated system for minimization Himani Raina (Mon Apr 22 2013 - 05:31:18 CDT)
- Re: solvated system for minimization karthik kumar (Mon Apr 22 2013 - 05:56:15 CDT)
- AW: solvated system for minimization Norman Geist (Mon Apr 22 2013 - 09:14:20 CDT)
Re: Link between simulations Suresh (Mon Apr 22 2013 - 01:37:00 CDT)
- Re: Link between simulations Thomas Evangelidis (Wed Apr 24 2013 - 04:30:12 CDT)
HEME acting unplanar Yarrow Madrona (Sun Apr 21 2013 - 17:48:43 CDT)
Link between simulations Mihaela Drenscko (Sat Apr 20 2013 - 15:18:36 CDT)
- AW: Link between simulations Norman Geist (Mon Apr 22 2013 - 01:34:43 CDT)
Computational Electrostatics for Biological Application (CEBA'13) - July 1-3 2013 - Genoa - Italy Walter Rocchia (Fri Apr 19 2013 - 04:59:23 CDT)
AW: floating point reproduceability Norman Geist (Fri Apr 19 2013 - 02:09:33 CDT)
Re: floating point reproduceability Thomas Brian (Thu Apr 18 2013 - 23:28:31 CDT)
- Re: floating point reproduceability Axel Kohlmeyer (Fri Apr 19 2013 - 03:02:11 CDT)
floating point reproduceability Thomas Brian (Wed Apr 17 2013 - 17:08:34 CDT)
- AW: floating point reproduceability Norman Geist (Thu Apr 18 2013 - 02:15:11 CDT)
NAMD "tCouple" option Tao Qu (Wed Apr 17 2013 - 15:56:54 CDT)
grcarma : a graphical user interface to carma Nicholas M Glykos (Wed Apr 17 2013 - 09:33:24 CDT)
Are coordinates in the tclForces module loaded as wrapped? Salvatore Mario Cosseddu (Tue Apr 16 2013 - 05:12:08 CDT)
total charge of the system - rounding error ? Fabien Cailliez (Mon Apr 15 2013 - 11:59:33 CDT)
- Re: total charge of the system - rounding error ? JC Gumbart (Mon Apr 15 2013 - 12:20:09 CDT)
Minimisation of protein in a water box Gareth Price (Sat Apr 13 2013 - 13:52:01 CDT)
- Re: Minimisation of protein in a water box Rajan Vatassery (Mon Apr 15 2013 - 12:30:46 CDT)
  - AW: Minimisation of protein in a water box Norman Geist (Tue Apr 16 2013 - 01:31:31 CDT)
restrain ligand to z-interval Magnus Andersson (Mon Apr 15 2013 - 06:29:07 CDT)
- Re: restrain ligand to z-interval Ajasja LjubetiÄ (Mon Apr 15 2013 - 08:22:07 CDT)
ABF karthik kumar (Mon Apr 15 2013 - 07:38:26 CDT)
restrain ligand in z-interval Magnus Andersson (Mon Apr 15 2013 - 06:37:26 CDT)
Problem with running FEP calculations Eric Lang (Sun Apr 14 2013 - 18:51:45 CDT)
- Re: Problem with running FEP calculations chipot (Mon Apr 15 2013 - 00:03:24 CDT)
  - RE: Problem with running FEP calculations Eric Lang (Mon Apr 15 2013 - 20:21:53 CDT)
ABF karthik kumar (Sat Apr 13 2013 - 06:45:12 CDT)
Inconsistency in fast table energy vs force Francesco Pietra (Sat Apr 13 2013 - 02:36:32 CDT)
- Fwd: Inconsistency in fast table energy vs force Francesco Pietra (Sat Apr 13 2013 - 05:27:01 CDT)
minimizer slowly moving atoms with bad contacts downhill Himani Raina (Fri Apr 12 2013 - 02:02:17 CDT)
- Re: minimizer slowly moving atoms with bad contacts downhill Axel Kohlmeyer (Fri Apr 12 2013 - 03:56:19 CDT)
Re: namd 2.9 tip4p-2005 Guanglei Cui (Thu Apr 11 2013 - 10:31:33 CDT)
pump / force application Arturas (Thu Apr 11 2013 - 08:19:46 CDT)
- Re: pump / force application Axel Kohlmeyer (Thu Apr 11 2013 - 08:23:10 CDT)
  - Re: pump / force application JÃ©rÃ´me HÃ©nin (Thu Apr 11 2013 - 08:15:14 CDT)
- Re: pump / force application Ivana (Thu Apr 11 2013 - 08:23:44 CDT)
Unsubscribe ÐÐ»ÐµÐºÑÐ°Ð½Ð´Ñ€ Ð¡ÐµÐ²ÐµÑ€ÑŽÑ…Ð¸Ð½ (Thu Apr 11 2013 - 01:45:51 CDT)
- Re: Unsubscribe Axel Kohlmeyer (Thu Apr 11 2013 - 03:43:00 CDT)
(no subject) Tina Stokelj (Thu Apr 11 2013 - 00:07:11 CDT)
Error in distributing the cores for a single processor Priyanka Purkayastha (Wed Apr 10 2013 - 23:36:00 CDT)
- Re: Error in distributing the cores for a single processor Axel Kohlmeyer (Thu Apr 11 2013 - 00:33:33 CDT)
  - Re: Error in distributing the cores for a single processor Axel Kohlmeyer (Thu Apr 11 2013 - 00:44:20 CDT)
  - AW: Error in distributing the cores for a single processor Norman Geist (Thu Apr 11 2013 - 01:20:57 CDT)
About Bond Deletion Vidhya Sankar (Wed Apr 10 2013 - 22:12:33 CDT)
- Re: About Bond Deletion Axel Kohlmeyer (Thu Apr 11 2013 - 00:32:45 CDT)
- AW: About Bond Deletion Norman Geist (Thu Apr 11 2013 - 00:57:43 CDT)
(no subject) Mohammad Jomah I Abu Saude (mbusaude) (Wed Apr 10 2013 - 17:30:08 CDT)
OpenMPI FEP Yields SegFaults and/or infinite dG Andrew Miglino (Wed Apr 10 2013 - 12:51:05 CDT)
tcf forces and ccordinate wrapping Arturas (Tue Apr 09 2013 - 13:23:21 CDT)
NAMD Output files Rawan Al Nsour (Tue Apr 09 2013 - 08:02:26 CDT)
- Re: NAMD Output files Axel Kohlmeyer (Thu Apr 11 2013 - 00:35:05 CDT)
ERROR: Constraint failure in RATTLE algorithm for atom 474! suresh satpati (Tue Apr 09 2013 - 00:54:41 CDT)
understanding which is which with GPU cards Francesco Pietra (Sat Apr 06 2013 - 17:17:13 CDT)
CUDA error in cuda_check_remote_progress on Pe 2 Francesco Pietra (Fri Apr 05 2013 - 09:55:44 CDT)
- Fwd: CUDA error in cuda_check_remote_progress on Pe 2 Francesco Pietra (Fri Apr 05 2013 - 09:58:58 CDT)
  - Fwd: CUDA error in cuda_check_remote_progress on Pe 2 Francesco Pietra (Fri Apr 05 2013 - 10:04:48 CDT)
    - Fwd: CUDA error in cuda_check_remote_progress on Pe 2 Francesco Pietra (Sat Apr 06 2013 - 04:49:21 CDT)
file for fixed atoms is not found! - but the file exist actually Sridhar Kumar Kannam (Thu Apr 04 2013 - 21:33:52 CDT)
- Re: file for fixed atoms is not found! - but the file exist actually Ramya Gamini (Fri Apr 05 2013 - 00:25:56 CDT)
  - Re: file for fixed atoms is not found! - but the file exist actually Sridhar Kumar Kannam (Fri Apr 05 2013 - 01:24:44 CDT)
  - Re: file for fixed atoms is not found! - but the file exist actually Rebecca Swett (Fri Apr 05 2013 - 09:23:54 CDT)
not fatal error but no more information Wang (Thu Apr 04 2013 - 13:50:17 CDT)
ABF karthik kumar (Thu Apr 04 2013 - 10:53:58 CDT)
- Re: ABF Giacomo Fiorin (Thu Apr 04 2013 - 11:24:57 CDT)
  - Re: ABF Giacomo Fiorin (Thu Apr 04 2013 - 16:09:15 CDT)
VDW component: NAMD vs. CHARMM Shubhra Ghosh Dastidar (Thu Apr 04 2013 - 09:20:23 CDT)
- Re: VDW component: NAMD vs. CHARMM JÃ©rÃ´me HÃ©nin (Thu Apr 04 2013 - 09:56:46 CDT)
pairInteraction and PME Jason Swails (Wed Apr 03 2013 - 15:58:21 CDT)
can't run multiple jobs with multiple gpus Gordon Wells (Wed Apr 03 2013 - 15:42:44 CDT)
- Re: can't run multiple jobs with multiple gpus Gordon Wells (Thu Apr 04 2013 - 19:10:02 CDT)
colvars configuration file example Martin, Erik W (Wed Apr 03 2013 - 15:04:41 CDT)
- Re: colvars configuration file example Giacomo Fiorin (Wed Apr 03 2013 - 15:09:12 CDT)
problem with inorganic builder genCompressedPsf Sridhar Kumar Kannam (Wed Apr 03 2013 - 01:05:07 CDT)
Sutton-Chen potential Zhao Lina (Mon Apr 01 2013 - 03:30:55 CDT)
- Re: Sutton-Chen potential Axel Kohlmeyer (Mon Apr 01 2013 - 03:40:43 CDT)
  - Re: Sutton-Chen potential Axel Kohlmeyer (Mon Apr 01 2013 - 04:30:19 CDT)
    - Re: Sutton-Chen potential Zhao Lina (Mon Apr 01 2013 - 22:09:28 CDT)
Unsubscribe Mark Cheeseman (Fri Mar 29 2013 - 23:05:32 CDT)
Timeline Mihaela Drenscko (Fri Mar 29 2013 - 19:20:41 CDT)
cuda error subbarao kanchi (Fri Mar 29 2013 - 12:36:50 CDT)
- Re: cuda error Aron Broom (Fri Mar 29 2013 - 18:40:46 CDT)
  - Re: cuda error subbarao kanchi (Sat Mar 30 2013 - 10:53:13 CDT)
- Re: cuda error subbarao kanchi (Mon Apr 08 2013 - 03:37:11 CDT)
Re: strange result using implicit solvent Niklaus Johner (Fri Mar 29 2013 - 08:39:05 CDT)
- Re: strange result using implicit solvent Branko (Fri Mar 29 2013 - 09:41:09 CDT)
  - Re: strange result using implicit solvent Aron Broom (Fri Mar 29 2013 - 12:04:43 CDT)
strange result using implicit solvent Fugui (Fri Mar 29 2013 - 08:00:04 CDT)
How to recenter a waterbox with ions around my protein? Maria Bykhovskaia (Thu Mar 28 2013 - 17:44:06 CDT)
- Re: How to recenter a waterbox with ions around my protein? Thomas Evangelidis (Fri Mar 29 2013 - 08:47:33 CDT)
Error in implicit solvent MD Fugui (Wed Mar 27 2013 - 15:08:19 CDT)
- Re: Error in implicit solvent MD Aron Broom (Wed Mar 27 2013 - 15:39:39 CDT)
2d periodic box Pavan G (Wed Mar 27 2013 - 12:51:25 CDT)
- Re: 2d periodic box Pavan G (Fri Mar 29 2013 - 08:39:59 CDT)
  - Re: 2d periodic box Pavan G (Fri Mar 29 2013 - 08:56:33 CDT)
    - Re: 2d periodic box Pavan G (Sun Mar 31 2013 - 12:50:49 CDT)
implicit solvent Fugui (Wed Mar 27 2013 - 11:27:55 CDT)
- Re: implicit solvent Axel Kohlmeyer (Wed Mar 27 2013 - 11:31:03 CDT)
  - Re: implicit solvent Aron Broom (Wed Mar 27 2013 - 12:20:30 CDT)
    - Re: implicit solvent Giacomo Fiorin (Wed Mar 27 2013 - 12:26:15 CDT)
    - Re: implicit solvent Aron Broom (Wed Mar 27 2013 - 12:30:09 CDT)
FFTK Atom types Francesco Pietra (Wed Mar 27 2013 - 02:21:13 CDT)
- Re: vmd-l: FFTK Atom types Mayne, Christopher G (Wed Mar 27 2013 - 08:06:05 CDT)
  - Re: vmd-l: FFTK Atom types Francesco Pietra (Wed Mar 27 2013 - 10:54:21 CDT)
NAMD post processing analysis.... linux freaker (Tue Mar 26 2013 - 21:09:31 CDT)
Accelerated MD parameters Gianluca Interlandi (Tue Mar 26 2013 - 19:37:56 CDT)
unsubscribe namd-l Bin Zhang (Tue Mar 26 2013 - 13:15:23 CDT)
(no subject) Mihaela Drenscko (Tue Mar 26 2013 - 12:41:35 CDT)
- Re: linux freaker (Tue Mar 26 2013 - 12:57:20 CDT)
  - Re: Aron Broom (Tue Mar 26 2013 - 13:02:52 CDT)
- Re: JÃ©rÃ´me HÃ©nin (Tue Mar 26 2013 - 12:35:01 CDT)
Final link of namd2 executable fails under AIX with xlC compiler Mark Cheeseman (Mon Mar 25 2013 - 17:07:05 CDT)
(no subject) Riley Workman (Mon Mar 25 2013 - 15:07:09 CDT)
- Re: JÃ©rÃ´me HÃ©nin (Mon Mar 25 2013 - 16:12:10 CDT)
  - Re: Aron Broom (Mon Mar 25 2013 - 16:48:45 CDT)
free energy methods cheat-sheet/comparison chart Thomas C. Bishop (Mon Mar 25 2013 - 13:49:16 CDT)
- Re: free energy methods cheat-sheet/comparison chart Aron Broom (Mon Mar 25 2013 - 14:28:00 CDT)
  - Re: free energy methods cheat-sheet/comparison chart Niklaus Johner (Mon Mar 25 2013 - 16:17:06 CDT)
    - Re: free energy methods cheat-sheet/comparison chart Aron Broom (Mon Mar 25 2013 - 16:43:54 CDT)
  - Re: free energy methods cheat-sheet/comparison chart Niklaus Johner (Mon Mar 25 2013 - 17:06:36 CDT)
    - Re: free energy methods cheat-sheet/comparison chart Giacomo Fiorin (Mon Mar 25 2013 - 17:11:29 CDT)
- Re: free energy methods cheat-sheet/comparison chart JC Gumbart (Mon Mar 25 2013 - 14:50:04 CDT)
  - Re: free energy methods cheat-sheet/comparison chart Thomas C. Bishop (Mon Mar 25 2013 - 14:56:11 CDT)
    - Re: free energy methods cheat-sheet/comparison chart Jeffrey Potoff (Mon Mar 25 2013 - 15:09:53 CDT)
    - RE: free energy methods cheat-sheet/comparison chart Dale l. Schruben (Mon Mar 25 2013 - 21:06:22 CDT)
Error with NAMD Energy Anurag Sharma (Mon Mar 25 2013 - 13:05:00 CDT)
Tetraphenylphosphonium Thomas Albers (Mon Mar 25 2013 - 12:19:31 CDT)
FEP OpenMPI Error Andrew Miglino (Fri Mar 22 2013 - 10:43:43 CDT)
Ligand in association with water Roy Fernando (Mon Mar 25 2013 - 09:40:44 CDT)
MARTINI Bad global angle count thomas lemmin (Mon Mar 25 2013 - 04:40:07 CDT)
Parameter file for DGEBA Sindu (Mon Mar 25 2013 - 03:56:40 CDT)
Morse potentail with charmm 27 Francesco Pietra (Sun Mar 24 2013 - 11:04:56 CDT)
Query regarding NAMD linux freaker (Sun Mar 24 2013 - 05:13:43 CDT)
Simulation at high pressure Rawan Al Nsour (Fri Mar 22 2013 - 14:20:49 CDT)
- Re: Simulation at high pressure Gianluca Interlandi (Fri Mar 22 2013 - 15:10:42 CDT)
  - Re: Simulation at high pressure Rawan Al Nsour (Sat Mar 23 2013 - 13:45:25 CDT)
Coordinate vs. time plots Mihaela Drenscko (Wed Mar 20 2013 - 17:17:46 CDT)
- AW: Coordinate vs. time plots Norman Geist (Thu Mar 21 2013 - 01:49:37 CDT)
- Re: Coordinate vs. time plots Mihaela Drenscko (Thu Mar 28 2013 - 06:11:44 CDT)
  - Re: Coordinate vs. time plots Ajasja LjubetiÄ (Thu Mar 28 2013 - 07:53:47 CDT)
Re: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? somedatta pal (Wed Mar 20 2013 - 00:37:21 CDT)
- AW: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? Norman Geist (Wed Mar 20 2013 - 02:47:06 CDT)
- Re: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? Grace Brannigan (Wed Mar 20 2013 - 08:45:51 CDT)
  - Re: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? somedatta pal (Thu Mar 21 2013 - 23:49:13 CDT)
MD crashes at 300K after warm up MD Patricia Campbell (Tue Mar 19 2013 - 13:30:23 CDT)
- AW: MD crashes at 300K after warm up MD Norman Geist (Wed Mar 20 2013 - 02:36:02 CDT)
how to switch off protein-water electrostatic interaction keeping the protein-water vdw interactions intact somedatta pal (Tue Mar 19 2013 - 02:57:09 CDT)
Fwd: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? somedatta pal (Tue Mar 19 2013 - 02:54:35 CDT)
- AW: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? Norman Geist (Tue Mar 19 2013 - 10:18:35 CDT)
AW: NamdMemoryReduction - genCompressedPsf Norman Geist (Tue Mar 19 2013 - 02:50:33 CDT)
Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? somedatta pal (Mon Mar 18 2013 - 23:58:43 CDT)
- Re: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? Axel Kohlmeyer (Tue Mar 19 2013 - 00:04:12 CDT)
  - Re: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? somedatta pal (Tue Mar 19 2013 - 00:35:22 CDT)
    - Re: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? Axel Kohlmeyer (Tue Mar 19 2013 - 01:15:42 CDT)
protein-water interactions somedatta pal (Mon Mar 18 2013 - 12:40:31 CDT)
Locally Enhanced Sampling Melina (Mon Mar 18 2013 - 12:20:09 CDT)
- Re: Locally Enhanced Sampling Melina (Wed Mar 27 2013 - 13:23:06 CDT)
distanceZ - harmonic restraints Narasimhan LOGANATHAN (Mon Mar 18 2013 - 12:14:46 CDT)
- Re: distanceZ - harmonic restraints JÃ©rÃ´me HÃ©nin (Mon Mar 18 2013 - 12:04:03 CDT)
  - Re: distanceZ - harmonic restraints Narasimhan LOGANATHAN (Mon Mar 18 2013 - 13:37:45 CDT)
- Re: distanceZ - harmonic restraints Aron Broom (Mon Mar 18 2013 - 12:35:47 CDT)
  - Re: distanceZ - harmonic restraints Narasimhan LOGANATHAN (Mon Mar 18 2013 - 13:38:55 CDT)
Restart simulation of an equilibrated bilayer with sugar molecules inserted Keller Wenger (Sun Mar 17 2013 - 09:51:27 CDT)
- AW: Restart simulation of an equilibrated bilayer with sugar molecules inserted Norman Geist (Mon Mar 18 2013 - 01:39:50 CDT)
smd force is too high Jacqueline Schmidt (Fri Mar 15 2013 - 11:25:58 CDT)
- Re: smd force is too high Aron Broom (Fri Mar 15 2013 - 12:10:55 CDT)
  - Re: smd force is too high Jacqueline Schmidt (Fri Mar 15 2013 - 12:35:52 CDT)
unsubscribe Van Ngo (Wed Mar 13 2013 - 18:23:14 CDT)
My calcforces does not work properly after a unknown point of the simulation. Salvatore Mario Cosseddu (Wed Mar 13 2013 - 15:35:11 CDT)
Effect of phi, psi cross term map (CMAP) correction on result of MD simulation dbaogen (Wed Mar 13 2013 - 04:13:42 CDT)
- Re: Effect of phi, psi cross term map (CMAP) correction on result of MD simulation Axel Kohlmeyer (Wed Mar 13 2013 - 04:20:08 CDT)
AW: LES very slow Norman Geist (Tue Mar 12 2013 - 01:51:40 CDT)
AW: NAMD 2.9 CUDA compilation Norman Geist (Tue Mar 12 2013 - 02:53:06 CDT)
Re: NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Mon Mar 11 2013 - 17:18:12 CDT)
- AW: NamdMemoryReduction - genCompressedPsf Norman Geist (Tue Mar 12 2013 - 01:58:11 CDT)
- Re: NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Thu Mar 21 2013 - 23:31:06 CDT)
  - AW: NamdMemoryReduction - genCompressedPsf Norman Geist (Fri Mar 22 2013 - 02:28:53 CDT)
- Re: NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Wed Apr 03 2013 - 00:05:39 CDT)
  - Re: NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Wed Apr 03 2013 - 01:00:06 CDT)
    - Re: NamdMemoryReduction - genCompressedPsf JC Gumbart (Wed Apr 03 2013 - 22:50:22 CDT)
    - Re: NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Thu Apr 04 2013 - 00:24:09 CDT)
NAMD 2.9 CUDA compilation Francesco Pietra (Mon Mar 11 2013 - 10:40:11 CDT)
- Fwd: NAMD 2.9 CUDA compilation Francesco Pietra (Mon Mar 11 2013 - 10:56:51 CDT)
  - AW: NAMD 2.9 CUDA compilation Norman Geist (Tue Mar 12 2013 - 01:57:00 CDT)
dynamic_cast cannot be done without runtime type information JÃ©rÃ´me HÃ©nin (Mon Mar 11 2013 - 10:16:24 CDT)
- Re: dynamic_cast cannot be done without runtime type information JÃ©rÃ´me HÃ©nin (Mon Mar 11 2013 - 10:31:27 CDT)
AW: NamdMemoryReduction - genCompressedPsf Norman Geist (Mon Mar 11 2013 - 01:56:40 CDT)
NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Sun Mar 10 2013 - 16:10:42 CDT)
Adding HEME parameters Yarrow Madrona (Sat Mar 09 2013 - 17:54:03 CST)
NAMD with Intel Xeon Phi coprocessors ? Christopher Neale (Fri Mar 08 2013 - 22:32:06 CST)
- AW: NAMD with Intel Xeon Phi coprocessors ? Norman Geist (Mon Mar 11 2013 - 02:05:28 CDT)
psf generation error Vasumathi Velachi (Fri Mar 08 2013 - 13:26:14 CST)
'Hands-on' Workshop on Computational Biophysics using VMD, NAMD, and ProDy, June 10-14, 2013 in Pittsburgh, PA David Brandon (Fri Mar 08 2013 - 12:08:25 CST)
NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Thu Mar 07 2013 - 21:39:20 CST)
- AW: NamdMemoryReduction - genCompressedPsf Norman Geist (Fri Mar 08 2013 - 01:04:34 CST)
memory demands of REMD Martin, Erik W (Thu Mar 07 2013 - 16:16:00 CST)
- Re: memory demands of REMD Chris Harrison (Thu Mar 07 2013 - 18:19:39 CST)
  - RE: memory demands of REMD Martin, Erik W (Thu Mar 07 2013 - 18:27:55 CST)
    - RE: memory demands of REMD Martin, Erik W (Fri Mar 08 2013 - 15:44:50 CST)
AW: LES very slow Norman Geist (Thu Mar 07 2013 - 00:47:59 CST)
using stackexchange was: Re: unsubscriber e-mail office pool anybody? Axel Kohlmeyer (Thu Mar 07 2013 - 03:04:16 CST)
tcl-related segfault in NAMD FX (Wed Mar 06 2013 - 09:32:39 CST)
- Re: tcl-related segfault in NAMD JÃ©rÃ´me HÃ©nin (Wed Mar 06 2013 - 09:33:07 CST)
  - Re: tcl-related segfault in NAMD FX (Wed Mar 06 2013 - 10:37:37 CST)
    - Re: tcl-related segfault in NAMD FX (Wed Mar 06 2013 - 12:59:37 CST)
AW: LES very slow Norman Geist (Wed Mar 06 2013 - 01:03:39 CST)
how to convert CHARMM TIP3P to traditional TIP3P subbarao kanchi (Wed Mar 06 2013 - 05:56:27 CST)
- Re: how to convert CHARMM TIP3P to traditional TIP3P Jeffrey Potoff (Wed Mar 06 2013 - 09:07:55 CST)
Fixing Langevin piston to allow off-diagonal stress (and why does the source say "FIX THIS"?) FX (Wed Mar 06 2013 - 04:43:49 CST)
- Re: Fixing Langevin piston to allow off-diagonal stress (and why does the source say "FIX THIS"?) FX (Wed Mar 06 2013 - 16:36:04 CST)
unsubscribe JC Gumbart (Tue Mar 05 2013 - 09:44:57 CST)
unsubscriber e-mail office pool anybody? Axel Kohlmeyer (Tue Mar 05 2013 - 07:11:44 CST)
- Re: unsubscriber e-mail office pool anybody? JÃ©rÃ´me HÃ©nin (Tue Mar 05 2013 - 07:02:47 CST)
  - Re: unsubscriber e-mail office pool anybody? Axel Kohlmeyer (Tue Mar 05 2013 - 08:36:45 CST)
  - Re: unsubscriber e-mail office pool anybody? Ajasja LjubetiÄ (Tue Mar 05 2013 - 08:39:01 CST)
- Re: unsubscriber e-mail office pool anybody? Aaron Oakley (Tue Mar 05 2013 - 07:31:42 CST)
unsubscribe karthik s (Tue Mar 05 2013 - 06:54:55 CST)
AW: LES very slow Norman Geist (Tue Mar 05 2013 - 00:08:42 CST)
problem in solvating a graphene layer created using VMD-nanotube builder Sridhar Kumar Kannam (Mon Mar 04 2013 - 21:37:15 CST)
- Re: problem in solvating a graphene layer created using VMD-nanotube builder Yi Wang, PhD (Mon Mar 04 2013 - 22:10:47 CST)
- AW: problem in solvating a graphene layer created using VMD-nanotube builder Norman Geist (Tue Mar 05 2013 - 00:18:44 CST)
remd run command question Martin, Erik W (Mon Mar 04 2013 - 12:59:56 CST)
- AW: remd run command question Norman Geist (Tue Mar 05 2013 - 00:14:22 CST)
unsubscribe Yihua Zhou (Mon Mar 04 2013 - 11:18:09 CST)
Very long simulation Mihaela Drenscko (Mon Mar 04 2013 - 05:55:07 CST)
- Re: Very long simulation Axel Kohlmeyer (Mon Mar 04 2013 - 06:10:43 CST)
  - Re: Very long simulation flavio seixas (Mon Mar 04 2013 - 17:39:26 CST)
NAMD PBS Parallel Job Error Aditya Ranganathan (Mon Mar 04 2013 - 03:44:15 CST)
AW: LES very slow Norman Geist (Mon Mar 04 2013 - 01:27:27 CST)
MDFF - should hydrogens be included? Geoffrey Kwai Wai Kong (Mon Mar 04 2013 - 00:19:26 CST)
unsubscribe Artem Zhmurov (Sat Mar 02 2013 - 03:12:14 CST)
Subject: Simulated Annealing/ Cooling Mariana Graterol (Fri Mar 01 2013 - 11:55:21 CST)
unsubscribe Purushottam Dixit (Fri Mar 01 2013 - 11:01:44 CST)
unsubscribe Riley Workman (Fri Mar 01 2013 - 10:59:39 CST)
unsubscribe rukman kesh (Fri Mar 01 2013 - 05:32:54 CST)
unsubscribe Shubhra Ghosh Dastidar (Fri Mar 01 2013 - 03:27:30 CST)
Protein Dielectric Constant in GBIS hanif mahboobi (Fri Mar 01 2013 - 02:58:01 CST)
- Protein Dielectric Constant in GBIS hanif mahboobi (Mon Mar 04 2013 - 12:31:46 CST)
unsubscribe karthik s (Fri Mar 01 2013 - 02:50:59 CST)
Fwd: NAMD + PLUMED COMPILATION Francesco Pietra (Fri Mar 01 2013 - 00:52:14 CST)
Sudden jumps during FEP Lewis Martin (Thu Feb 28 2013 - 23:16:21 CST)
Amorphous Structure code or builder Rawan Al Nsour (Thu Feb 28 2013 - 14:47:14 CST)
NAMD + PLUMED COMPILATION Francesco Pietra (Thu Feb 28 2013 - 11:02:28 CST)
- Re: NAMD + PLUMED COMPILATION Giacomo Fiorin (Thu Feb 28 2013 - 11:26:00 CST)
(no subject) Francesco Pietra (Thu Feb 28 2013 - 10:59:57 CST)
converting dcd files to netcdf or ascii Daniel Abergel (Thu Feb 28 2013 - 07:04:41 CST)
- AW: converting dcd files to netcdf or ascii Norman Geist (Thu Feb 28 2013 - 09:05:59 CST)
GPUs silently stop working during simulation when oversubscribed Benjamin Merget (Thu Feb 28 2013 - 02:51:39 CST)
- AW: GPUs silently stop working during simulation when oversubscribed Norman Geist (Thu Feb 28 2013 - 03:21:00 CST)
  - Re: GPUs silently stop working during simulation when oversubscribed Benjamin Merget (Thu Feb 28 2013 - 04:04:30 CST)
    - AW: GPUs silently stop working during simulation when oversubscribed Norman Geist (Thu Feb 28 2013 - 05:41:04 CST)
AW: LES very slow Norman Geist (Thu Feb 28 2013 - 00:37:07 CST)
colvar keyword ForceNoPBC Nadeem A. Vellore (Wed Feb 27 2013 - 23:46:09 CST)
- Re: colvar keyword ForceNoPBC Giacomo Fiorin (Wed Feb 27 2013 - 23:50:16 CST)
ABF - distance between two domains Nadeem A. Vellore (Wed Feb 27 2013 - 15:12:35 CST)
- Re: ABF - distance between two domains Nadeem A. Vellore (Wed Feb 27 2013 - 15:45:49 CST)
(no subject) Moema Monteiro (Wed Feb 27 2013 - 15:08:10 CST)
Re: NAMD on Stampede Niklaus Johner (Wed Feb 27 2013 - 14:27:34 CST)
NAMD on Stampede hanif mahboobi (Wed Feb 27 2013 - 13:46:29 CST)
- RE: NAMD on Stampede Zumot, Elia Nabil (Wed Feb 27 2013 - 14:15:51 CST)
MDFF volumetric map Ivana (Wed Feb 27 2013 - 11:43:03 CST)
smd simulation Jacqueline Schmidt (Wed Feb 27 2013 - 08:27:43 CST)
- AW: smd simulation Norman Geist (Thu Feb 28 2013 - 00:48:19 CST)
  - Re: AW: smd simulation Jacqueline Schmidt (Thu Feb 28 2013 - 01:12:36 CST)
    - AW: AW: smd simulation Norman Geist (Thu Feb 28 2013 - 03:10:01 CST)
About PLUMED with NAMD VMD Francesco Pietra (Wed Feb 27 2013 - 02:16:28 CST)
- Re: About PLUMED with NAMD VMD Giacomo Fiorin (Wed Feb 27 2013 - 02:39:27 CST)
- Re: About PLUMED with NAMD VMD davide branduardi (Wed Feb 27 2013 - 02:41:14 CST)
- Re: vmd-l: About PLUMED with NAMD VMD John Stone (Wed Feb 27 2013 - 10:10:48 CST)
  - Re: vmd-l: About PLUMED with NAMD VMD andrea spitaleri (Thu Feb 28 2013 - 02:46:34 CST)
AW: RATTLE algorithm Norman Geist (Wed Feb 27 2013 - 01:24:05 CST)
AW: LES very slow Norman Geist (Wed Feb 27 2013 - 01:19:51 CST)
RE: DCD file doubles a monomer JC Gumbart (Tue Feb 26 2013 - 20:58:04 CST)
DCD file doubles a monomer Patricia Campbell (Tue Feb 26 2013 - 15:01:18 CST)
DCD file doubles a monomer Patricia Campbell (Tue Feb 26 2013 - 12:09:16 CST)
- Re: DCD file doubles a monomer Patricia Campbell (Tue Feb 26 2013 - 12:13:53 CST)
  - Re: DCD file doubles a monomer Aron Broom (Tue Feb 26 2013 - 12:34:54 CST)
  - Re: DCD file doubles a monomer Eduard Schreiner (Tue Feb 26 2013 - 16:17:34 CST)
- Re: DCD file doubles a monomer JC Gumbart (Tue Feb 26 2013 - 19:50:08 CST)
Simulated Annealing/ Cooling Rawan Al Nsour (Tue Feb 26 2013 - 09:43:32 CST)
Regarding installing Namd 2.9 on windows xp 32 bit system Himani Raina (Tue Feb 26 2013 - 04:08:25 CST)
- AW: Regarding installing Namd 2.9 on windows xp 32 bit system Norman Geist (Wed Feb 27 2013 - 01:30:58 CST)
LES very slow Siri Søndergaard (Mon Feb 25 2013 - 18:00:02 CST)
- AW: LES very slow Norman Geist (Tue Feb 26 2013 - 00:42:30 CST)
RATTLE algorithm Mihaela Drenscko (Mon Feb 25 2013 - 17:56:25 CST)
- AW: RATTLE algorithm Norman Geist (Tue Feb 26 2013 - 00:38:53 CST)
ABF thermostats and energy introduced into the system Ajasja LjubetiÄ (Mon Feb 25 2013 - 07:07:39 CST)
- Re: ABF thermostats and energy introduced into the system JÃ©rÃ´me HÃ©nin (Mon Feb 25 2013 - 08:01:52 CST)
  - Re: ABF thermostats and energy introduced into the system Ajasja LjubetiÄ (Tue Feb 26 2013 - 03:10:27 CST)
  - Re: ABF thermostats and energy introduced into the system Ajasja LjubetiÄ (Wed Feb 27 2013 - 06:26:39 CST)
- Re: ABF thermostats and energy introduced into the system JC Gumbart (Mon Feb 25 2013 - 16:32:13 CST)
  - Re: ABF thermostats and energy introduced into the system Ajasja LjubetiÄ (Tue Feb 26 2013 - 02:52:54 CST)
  - Re: ABF thermostats and energy introduced into the system Ajasja LjubetiÄ (Wed Feb 27 2013 - 11:29:28 CST)
    - Re: ABF thermostats and energy introduced into the system JC Gumbart (Wed Feb 27 2013 - 15:29:49 CST)
Re: Always 24-way SMP? Andrew Pearson (Mon Feb 25 2013 - 06:28:05 CST)
- AW: Always 24-way SMP? Norman Geist (Mon Feb 25 2013 - 09:06:05 CST)
- Re: Always 24-way SMP? Andrew Pearson (Mon Feb 25 2013 - 11:50:13 CST)
  - AW: Always 24-way SMP? Norman Geist (Tue Feb 26 2013 - 00:27:27 CST)
- Re: Always 24-way SMP? Andrew Pearson (Tue Feb 26 2013 - 08:14:52 CST)
  - AW: Always 24-way SMP? Norman Geist (Wed Feb 27 2013 - 01:53:27 CST)
Calculate binding free energy yp sun (Sun Feb 24 2013 - 19:22:08 CST)
- Re: Calculate binding free energy Aron Broom (Sun Feb 24 2013 - 22:46:17 CST)
spectrum simulation francesco oteri (Sun Feb 24 2013 - 14:56:55 CST)
- AW: spectrum simulation Norman Geist (Mon Feb 25 2013 - 01:01:05 CST)
center of mass calculation in the tcl interface Jacqueline Schmidt (Sun Feb 24 2013 - 13:02:21 CST)
- Re: center of mass calculation in the tcl interface Aron Broom (Sun Feb 24 2013 - 14:48:38 CST)
Single point energy calc with gaussian/namd... log file interpretation Stober, Spencer T (Fri Feb 22 2013 - 16:31:01 CST)
- Re: Single point energy calc with gaussian/namd... log file interpretation Axel Kohlmeyer (Sat Feb 23 2013 - 02:30:10 CST)
Always 24-way SMP? Andrew Pearson (Fri Feb 22 2013 - 12:29:58 CST)
- AW: Always 24-way SMP? Norman Geist (Mon Feb 25 2013 - 00:55:26 CST)
(no subject) Titis Sekar Humani (Fri Feb 22 2013 - 00:05:07 CST)
- Re: amin_at_imtech.res.in (Fri Feb 22 2013 - 00:31:16 CST)
- AW: Norman Geist (Fri Feb 22 2013 - 00:49:17 CST)
  - Re: AW: Titis Sekar Humani (Fri Feb 22 2013 - 00:57:11 CST)
Epoxy CHARMM Rawan Al Nsour (Thu Feb 21 2013 - 18:11:41 CST)
Re: Orientation colvar + metadynamics questions Benjamin Bouvier (Thu Feb 21 2013 - 07:37:06 CST)
- Re: Orientation colvar + metadynamics questions JÃ©rÃ´me HÃ©nin (Thu Feb 21 2013 - 09:21:43 CST)
  - Re: Orientation colvar + metadynamics questions Giacomo Fiorin (Thu Feb 21 2013 - 10:10:24 CST)
Orientation colvar + metadynamics questions Benjamin Bouvier (Thu Feb 21 2013 - 04:58:48 CST)
How to write dcd file within Tclforce script Teerapong Pirojsirikul (Wed Feb 20 2013 - 17:56:31 CST)
Collective variable data analysis using WHAM Narasimhan LOGANATHAN (Wed Feb 20 2013 - 11:55:31 CST)
Polarizability Question! Sai Kumar Ramadugu (Wed Feb 20 2013 - 11:46:06 CST)
topology/parameter files for biotin Sridhar Kumar Kannam (Tue Feb 19 2013 - 21:27:48 CST)
Constant volume energy minimization FX (Tue Feb 19 2013 - 16:06:53 CST)
- Re: Constant volume energy minimization Michael Mazack (Tue Feb 19 2013 - 16:18:00 CST)
  - Re: Constant pressure energy minimization FX (Wed Feb 20 2013 - 02:18:43 CST)
- Re: Constant volume energy minimization JÃ©rÃ´me HÃ©nin (Wed Feb 20 2013 - 04:29:50 CST)
NAMD 2.9 jobs hanging. Bhupender Thakur (Mon Feb 18 2013 - 20:40:14 CST)
transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin Izhar Karbat (Mon Feb 18 2013 - 11:26:30 CST)
- Re: transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin francesco oteri (Mon Feb 18 2013 - 11:31:09 CST)
- RE: transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin Zumot, Elia Nabil (Mon Feb 18 2013 - 11:49:35 CST)
namd2 CUDA errors for non-superusers in Debian Blake Mertz (Thu Feb 14 2013 - 16:28:23 CST)
- Re: namd2 CUDA errors for non-superusers in Debian Aron Broom (Thu Feb 14 2013 - 17:31:26 CST)
  - Re: namd2 CUDA errors for non-superusers in Debian Blake Mertz (Fri Feb 15 2013 - 08:42:57 CST)
Scaling on 64 core nodes? Rebecca Swett (Thu Feb 14 2013 - 08:37:44 CST)
- AW: Scaling on 64 core nodes? Norman Geist (Fri Feb 15 2013 - 01:43:58 CST)
confines volume effects Martin, Erik W (Thu Feb 14 2013 - 12:30:39 CST)
- Re: confines volume effects Nicholas M Glykos (Fri Feb 15 2013 - 04:04:29 CST)
Re: running NAMD on Amazon EC2? Ajasja LjubetiÄ (Thu Feb 14 2013 - 02:39:06 CST)
- Re: running NAMD on Amazon EC2? Cloud Computing (Thu Feb 14 2013 - 14:38:38 CST)
- Re: running NAMD on Amazon EC2? Cloud Computing (Thu Feb 14 2013 - 14:48:04 CST)
  - Re: running NAMD on Amazon EC2? Axel Kohlmeyer (Thu Feb 14 2013 - 14:53:56 CST)
running NAMD on Amazon EC2? Cloud Computing (Wed Feb 13 2013 - 16:05:03 CST)
- AW: running NAMD on Amazon EC2? Norman Geist (Thu Feb 14 2013 - 01:30:58 CST)
- Re: running NAMD on Amazon EC2? Dong Luo (Thu Feb 14 2013 - 10:54:21 CST)
SOLVED: Fatal Error by charmc.../usr/bin/ld: cannot find -lsrfftw. Please help! Jose Borreguero (Wed Feb 13 2013 - 12:34:49 CST)
Fatal Error by charmc.../usr/bin/ld: cannot find -lsrfftw. Please help! Jose Borreguero (Tue Feb 12 2013 - 17:26:12 CST)
Simulation continuously crashes after minimization Patricia Campbell (Tue Feb 12 2013 - 15:01:37 CST)
- RE: Simulation continuously crashes after minimization Cruz-Chu Eduardo Roberto (Tue Feb 12 2013 - 17:00:57 CST)
Simulation continuously crashes after minimization Patricia Campbell (Tue Feb 12 2013 - 14:52:03 CST)
Namd and CUDA on Debian Wheezy Vlastimil ZÃma (Tue Feb 12 2013 - 07:11:38 CST)
Apply torque with NAMD George Patargias (Tue Feb 12 2013 - 05:30:28 CST)
- Re: Apply torque with NAMD JÃ©rÃ´me HÃ©nin (Tue Feb 12 2013 - 07:08:35 CST)
Repelling extracellular regions of the protein from membrane in NAMD MD simulation Sahu, Indra (Sat Feb 09 2013 - 14:58:24 CST)
Generating topology files for crystalline materials FX (Sun Feb 10 2013 - 12:05:26 CST)
- Re: Generating topology files for crystalline materials Axel Kohlmeyer (Sun Feb 10 2013 - 12:22:09 CST)
  - Re: Generating topology files for crystalline materials FX (Sun Feb 10 2013 - 14:02:16 CST)
Repelling extracellular regions of the protein from membrane in NAMD MD simulation Sahu, Indra (Sun Feb 10 2013 - 11:43:43 CST)
How to get cell information from within calcforces in TclForces Salvatore Mario Cosseddu (Fri Feb 08 2013 - 17:35:52 CST)
Current CVS broken? (SortedArray.h) Michael Mazack (Tue Feb 05 2013 - 12:52:26 CST)
- Re: Current CVS broken? (SortedArray.h) Chris Harrison (Tue Feb 05 2013 - 13:20:58 CST)
  - Re: Current CVS broken? (SortedArray.h) Michael Mazack (Tue Feb 05 2013 - 14:24:42 CST)
    - Re: Current CVS broken? (SortedArray.h) Michael Mazack (Wed Feb 06 2013 - 09:00:43 CST)
Simulated Annealing for a polymer Rawan Al Nsour (Mon Feb 04 2013 - 13:13:54 CST)
ERROR: Constraint failure in RATTLE algorithm for atom 593! Nutan Preety (Mon Feb 04 2013 - 06:26:44 CST)
- AW: ERROR: Constraint failure in RATTLE algorithm for atom 593! Norman Geist (Mon Feb 04 2013 - 09:33:08 CST)
Re: namd-l digest V1 #979 Nutan Preety (Mon Feb 04 2013 - 06:18:55 CST)
unsubscribe Elif Ozkirimli (Sun Feb 03 2013 - 17:34:25 CST)
SMD and torque application George Patargias (Sun Feb 03 2013 - 14:42:09 CST)
NAMD mailing list unsubscribe instructions Ajasja LjubetiÄ (Sun Feb 03 2013 - 11:28:32 CST)
unsubscribe Purushottam Dixit (Sun Feb 03 2013 - 07:38:18 CST)
- unsubscribe shivani nanda (Sun Feb 03 2013 - 11:02:28 CST)
  - unsubscribe shivani nanda (Sun Feb 03 2013 - 11:02:57 CST)
unsubscribe Tina Stokelj (Sat Feb 02 2013 - 00:02:14 CST)
- unsubscribe Mahdi Tavakol (Sun Feb 03 2013 - 02:52:04 CST)
unsubscribe Elif Ozkirimli (Fri Feb 01 2013 - 18:37:04 CST)
- unsubscribe Benjamin Hill (Sat Feb 02 2013 - 01:19:41 CST)
  - unsubscribe Benjamin Hill (Sat Feb 02 2013 - 01:19:58 CST)
Does NAMD read the PDB element field? Albrecht Goez (Fri Feb 01 2013 - 02:52:15 CST)
Cellulose MD simulations Patriche Simona (Thu Jan 31 2013 - 04:39:33 CST)
- Re: Cellulose MD simulations Munir S. Skaf (Fri Feb 01 2013 - 07:46:07 CST)
direction of pull in namd raghav singh (Tue Jan 29 2013 - 07:18:49 CST)
- Re: direction of pull in namd Leandro Martínez (Tue Jan 29 2013 - 08:09:01 CST)
  - Re: direction of pull in namd Leandro Martínez (Tue Jan 29 2013 - 10:46:15 CST)
Re: Percentage of Residues in Ramachandran Plot regions versus time of trajectory Aditya Ranganathan (Tue Jan 29 2013 - 04:14:57 CST)
- AW: Percentage of Residues in Ramachandran Plot regions versus time of trajectory Norman Geist (Tue Jan 29 2013 - 08:27:01 CST)
- Re: Percentage of Residues in Ramachandran Plot regions versus time of trajectory Aditya Ranganathan (Tue Jan 29 2013 - 09:51:31 CST)
Problem with psfgen for Carbohydrates Sai Kumar Ramadugu (Mon Jan 28 2013 - 13:28:06 CST)
- Re: Problem with psfgen for Carbohydrates Aaron Oakley (Mon Jan 28 2013 - 16:53:24 CST)
Metadynamics pmf restart Riley Workman (Mon Jan 28 2013 - 12:18:48 CST)
- Re: Metadynamics pmf restart Giacomo Fiorin (Mon Jan 28 2013 - 14:43:56 CST)
Re: Question about NAMD johan strumpfer (Mon Jan 28 2013 - 02:02:13 CST)
- AW: Re: Question about NAMD Norman Geist (Tue Jan 29 2013 - 00:24:26 CST)
Percentage of Residues in Ramachandran Plot regions versus time of trajectory Aditya Ranganathan (Sun Jan 27 2013 - 22:45:13 CST)
- AW: Percentage of Residues in Ramachandran Plot regions versus time of trajectory Norman Geist (Mon Jan 28 2013 - 00:08:17 CST)
not reading improper angle from amber1.5 ff12SB Jorgen Simonsen (Sun Jan 27 2013 - 16:06:20 CST)
(no subject) forough askari (Sun Jan 27 2013 - 10:06:36 CST)
suppressing LBD output Jorgen Simonsen (Sat Jan 26 2013 - 21:57:18 CST)
How to split large NAMD DCD file snoze pa (Thu Jan 24 2013 - 10:49:58 CST)
- Re: How to split large NAMD DCD file Aron Broom (Thu Jan 24 2013 - 11:06:45 CST)
- Re: How to split large NAMD DCD file Michael Purdy (Thu Jan 24 2013 - 11:06:33 CST)
- Re: How to split large NAMD DCD file flavio seixas (Thu Jan 24 2013 - 11:09:31 CST)
- Re: How to split large NAMD DCD file Branko (Thu Jan 24 2013 - 11:15:17 CST)
question regarding interaction parameters subbarao kanchi (Thu Jan 24 2013 - 09:52:42 CST)
- Re: question regarding interaction parameters Victor Ovchinnikov (Thu Jan 24 2013 - 10:37:22 CST)
  - Re: question regarding interaction parameters subbarao kanchi (Thu Jan 24 2013 - 12:36:57 CST)
Assigning Partial Charges to FE in Active Site Superoxide Dismutase. Roy Fernando (Wed Jan 23 2013 - 13:39:04 CST)
- AW: Assigning Partial Charges to FE in Active Site Superoxide Dismutase. Norman Geist (Thu Jan 24 2013 - 01:23:18 CST)
Using CNS parameter file to create NAMD topology and parameter files Roy Fernando (Wed Jan 23 2013 - 13:21:35 CST)
Re: FEP on an amino acid ligand Thomas Albers (Tue Jan 22 2013 - 16:36:59 CST)
- AW: FEP on an amino acid ligand Norman Geist (Wed Jan 23 2013 - 01:21:09 CST)
- Re: FEP on an amino acid ligand Thomas Albers (Wed Jan 23 2013 - 07:36:36 CST)
  - Re: FEP on an amino acid ligand JÃ©rÃ´me HÃ©nin (Wed Jan 23 2013 - 08:13:30 CST)
    - Re: FEP on an amino acid ligand Thomas Albers (Wed Jan 23 2013 - 09:30:36 CST)
  - Re: FEP on an amino acid ligand JC Gumbart (Wed Jan 23 2013 - 08:24:25 CST)
- Re: FEP on an amino acid ligand JC Gumbart (Wed Jan 23 2013 - 11:16:32 CST)
- Re: FEP on an amino acid ligand JC Gumbart (Wed Jan 23 2013 - 11:29:57 CST)
  - Re: FEP on an amino acid ligand Gordon Wells (Wed Jan 23 2013 - 14:44:41 CST)
(no subject) forough askari (Tue Jan 22 2013 - 16:32:34 CST)
FEP on an amino acid ligand Thomas Albers (Mon Jan 21 2013 - 19:44:20 CST)
- AW: FEP on an amino acid ligand Norman Geist (Tue Jan 22 2013 - 00:28:38 CST)
(no subject) forough askari (Mon Jan 21 2013 - 18:38:10 CST)
About "add solvation" Francesco Pietra (Mon Jan 21 2013 - 03:42:54 CST)
- Fwd: About "add solvation" Francesco Pietra (Mon Jan 21 2013 - 03:49:06 CST)
Remove tjwang@iastate.edu from the list pls Norman Geist (Mon Jan 21 2013 - 00:04:57 CST)
smd tcl script - problem atoms id Branko (Sun Jan 20 2013 - 10:37:56 CST)
- Re: smd tcl script - problem atoms id Branko (Sun Jan 20 2013 - 16:46:56 CST)
Running namd on linux in cpu+gpu mode James Starlight (Sat Jan 19 2013 - 01:19:53 CST)
- AW: Running namd on linux in cpu+gpu mode Norman Geist (Sun Jan 20 2013 - 23:52:48 CST)
H-bonds cutoff angle criterian Anurag Sharma (Thu Jan 17 2013 - 20:52:40 CST)
- H-bonds cutoff angle criterian Anurag Sharma (Sun Jan 20 2013 - 10:54:07 CST)
  - AW: H-bonds cutoff angle criterian Norman Geist (Sun Jan 20 2013 - 23:46:48 CST)
    - Re: AW: H-bonds cutoff angle criterian. . Martin, Erik W (Mon Jan 21 2013 - 01:07:11 CST)
    - Re: AW: H-bonds cutoff angle criterian. . Anurag Sharma (Mon Jan 21 2013 - 01:11:46 CST)
Scaling problem: 4 nodes OK, 5 fails to start Stober, Spencer T (Wed Jan 16 2013 - 13:39:08 CST)
- AW: Scaling problem: 4 nodes OK, 5 fails to start Norman Geist (Thu Jan 17 2013 - 00:14:37 CST)
  - RE: Scaling problem: 4 nodes OK, 5 fails to start Stober, Spencer T (Thu Jan 17 2013 - 08:31:53 CST)
    - AW: Scaling problem: 4 nodes OK, 5 fails to start Norman Geist (Mon Jan 21 2013 - 00:02:25 CST)
Scaling problem: 4 nodes OK, 5 nodes fail Stober, Spencer T (Wed Jan 16 2013 - 13:46:07 CST)
src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target Paraskevi Gkeka (Wed Jan 16 2013 - 10:29:52 CST)
- src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target Paraskevi Gkeka (Wed Jan 16 2013 - 10:35:57 CST)
- Re: src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target David Hardy (Wed Jan 16 2013 - 11:07:48 CST)
Re: Re: AW: AW: CUDA problem? Ajasja LjubetiÄ (Wed Jan 16 2013 - 10:04:02 CST)
- AW: Re: AW: AW: CUDA problem? Norman Geist (Thu Jan 17 2013 - 00:01:27 CST)
topology file for ligand Maria Saeed (Wed Jan 16 2013 - 01:47:34 CST)
- Re: topology file for ligand Aaron Oakley (Wed Jan 16 2013 - 02:11:07 CST)
DNA terminals and charges Siri Søndergaard (Tue Jan 15 2013 - 20:45:40 CST)
- Re: DNA terminals and charges Jack Bulat (Tue Jan 15 2013 - 22:13:24 CST)
NAMD with NVIDIA Quadro K5000? Martin, Erik W (Tue Jan 15 2013 - 12:15:41 CST)
Re: AW: AW: CUDA problem? Eric Hill (Tue Jan 15 2013 - 01:12:53 CST)
- AW: Re: AW: AW: CUDA problem? Norman Geist (Wed Jan 16 2013 - 00:21:57 CST)
namd 2.9 tip4p-2005 Daniele Gentili (Tue Jan 15 2013 - 06:23:14 CST)
- AW: namd 2.9 tip4p-2005 Norman Geist (Wed Jan 16 2013 - 00:01:40 CST)
DNA surrounded by a shell of water in a big box with vacuum Bikan Tan (Mon Jan 14 2013 - 11:01:06 CST)
- AW: DNA surrounded by a shell of water in a big box with vacuum Norman Geist (Tue Jan 15 2013 - 00:39:59 CST)
  - (no subject) Maria Saeed (Tue Jan 15 2013 - 01:03:27 CST)
    - How we can merge protein and ligand complex? Maria Saeed (Tue Jan 15 2013 - 01:06:20 CST)
    - Re: How we can merge protein and ligand complex? Eric Hill (Tue Jan 15 2013 - 01:15:22 CST)
Martini RBCG DENILSON FERREIRA DE OLIVEIRA (Mon Jan 14 2013 - 09:55:51 CST)
CNT coarse grain hamid mosaddeghi (Fri Jan 11 2013 - 06:01:51 CST)
- Re: CNT coarse grain Ramin Ekhteiari (Sat Jan 12 2013 - 03:29:59 CST)
NAMD on Stempede (and other MIC Coprocessor systems) Jeff Wereszczynski (Fri Jan 11 2013 - 13:39:37 CST)
- Re: NAMD on Stempede (and other MIC Coprocessor systems) Chris Harrison (Fri Jan 11 2013 - 15:18:42 CST)
Charm 6.5.0 compilation issue Dmitry Osolodkin (Fri Jan 11 2013 - 07:17:21 CST)
- Re: [charm] Charm 6.5.0 compilation issue Ake Sandgren (Fri Jan 11 2013 - 12:21:43 CST)
Re: secondary structure analysis Nicholas M Glykos (Fri Jan 11 2013 - 02:57:26 CST)
- Re: secondary structure analysis Ajasja LjubetiÄ (Fri Jan 11 2013 - 03:34:55 CST)
secondary structure analysis Martin, Erik W (Wed Jan 09 2013 - 14:20:36 CST)
- AW: secondary structure analysis Norman Geist (Thu Jan 10 2013 - 00:16:07 CST)
Switching function while using AMBER force field Sneha Menon (Wed Jan 09 2013 - 04:03:09 CST)
Charm 6.5.0 compilation issue Dmitry Osolodkin (Sun Jan 06 2013 - 13:28:27 CST)
How Pressureprofile output are averaged ? namd_chcwaaa_at_yahoo.com.cn (Fri Jan 04 2013 - 23:21:39 CST)
NAMD 2.9 Replica-exchange. FATAL ERROR: Unknown command-line option +replicas ncskocze_at_cyf-kr.edu.pl (Fri Jan 04 2013 - 07:53:16 CST)
SOLVED: Issues with the "Keep Water Out" tcl script B Hartzoulakis (Fri Jan 04 2013 - 05:01:08 CST)
- FW: SOLVED: Issues with the "Keep Water Out" tcl script B Hartzoulakis (Fri Jan 04 2013 - 05:14:29 CST)
namd-I: sub-routine code in NAMD goldwheel87 (Thu Jan 03 2013 - 16:18:27 CST)
- Re: namd-I: sub-routine code in NAMD Axel Kohlmeyer (Thu Jan 03 2013 - 21:05:51 CST)
RE: Issues with the "Keep Water Out" tcl script peter.schmidtke_at_fr.netgrs.com (Thu Jan 03 2013 - 09:09:29 CST)
Issues with the "Keep Water Out" tcl script B Hartzoulakis (Thu Jan 03 2013 - 06:15:50 CST)
WHAM in the NPT ensemble Shaon Chakrabarti (Mon Dec 31 2012 - 14:35:50 CST)
loop-to-helix change during SMD yp sun (Mon Dec 31 2012 - 05:17:53 CST)
Compiling NAMD 2.9 on BlueGene/Q Vasudevan V (Wed Dec 26 2012 - 17:11:17 CST)
Namd 2.9 on a BlueGene/Q machine Vasudevan V (Wed Dec 26 2012 - 17:29:34 CST)
smd-tclForce intrerface Jacqueline Schmidt (Wed Dec 26 2012 - 12:04:23 CST)
discrepancy in results from different machines! Jacqueline Schmidt (Tue Dec 25 2012 - 17:29:05 CST)
- Re: discrepancy in results from different machines! Thomas Evangelidis (Tue Dec 25 2012 - 17:56:16 CST)
How to improve the GPU utility in NAMD Íõ¾ü (Tue Dec 25 2012 - 02:35:06 CST)
- Re: How to improve the GPU utility in NAMD Thomas Evangelidis (Tue Dec 25 2012 - 04:33:56 CST)
Namd: nohup: ignoring input and redirecting stderr to stdout Maria Saeed (Mon Dec 24 2012 - 00:30:32 CST)
- Re: Namd: nohup: ignoring input and redirecting stderr to stdout Axel Kohlmeyer (Mon Dec 24 2012 - 01:18:10 CST)
First impressions from AMBER ff12SB ? Nicholas M Glykos (Sun Dec 23 2012 - 10:58:36 CST)
reassigning temperatures Martin, Erik W (Thu Dec 20 2012 - 11:40:36 CST)
- RE: reassigning temperatures Martin, Erik W (Thu Jan 03 2013 - 08:19:24 CST)
Behavior of explicit water beyond periodic boundaries Dr. Eddie (Thu Dec 20 2012 - 11:03:02 CST)
- Re: Behavior of explicit water beyond periodic boundaries Dr. Eddie (Thu Dec 20 2012 - 11:42:31 CST)
- Re: Behavior of explicit water beyond periodic boundaries Aron Broom (Thu Dec 20 2012 - 11:56:11 CST)
  - Re: Behavior of explicit water beyond periodic boundaries Aron Broom (Thu Dec 20 2012 - 11:56:30 CST)
Switching function while using AMBER force field Sneha Menon (Thu Dec 20 2012 - 00:06:25 CST)
charging free energies with alchdecouple Harris, Robert C. (Wed Dec 19 2012 - 11:29:08 CST)
- Re: charging free energies with alchdecouple Ali Khanlarkhani (Wed Dec 19 2012 - 13:06:40 CST)
  - Re: charging free energies with alchdecouple JÃ©rÃ´me HÃ©nin (Thu Dec 20 2012 - 03:06:05 CST)
    - RE: charging free energies with alchdecouple Harris, Robert C. (Fri Dec 21 2012 - 12:44:42 CST)
cylinder constraint with colvar Wang (Tue Dec 18 2012 - 11:42:28 CST)
- Re: cylinder constraint with colvar Aron Broom (Tue Dec 18 2012 - 15:31:25 CST)
  - Re: cylinder constraint with colvar Aron Broom (Tue Dec 18 2012 - 23:19:54 CST)
How to parameterize Protein ligand complex in membrane? Maria Saeed (Mon Dec 17 2012 - 22:54:06 CST)
- How to parameterize Protein ligand complex in membrane? Maria Saeed (Tue Dec 18 2012 - 00:04:08 CST)
Re: namd-l digest V1 #949 Nicholas M Glykos (Mon Dec 17 2012 - 04:06:22 CST)
Adaptive Tempering "OPENING EXTENDED SYSTEM TRAJECTORY FILE" error Siri Søndergaard (Sun Dec 16 2012 - 22:53:31 CST)
GPU acceleration by using ATI video card dongsheng lei (Fri Dec 14 2012 - 02:28:13 CST)
- Re: GPU acceleration by using ATI video card Aron Broom (Fri Dec 14 2012 - 02:49:04 CST)
  - Re: GPU acceleration by using ATI video card Axel Kohlmeyer (Fri Dec 14 2012 - 02:56:14 CST)
  - Re: GPU acceleration by using ATI video card Axel Kohlmeyer (Fri Dec 14 2012 - 03:04:27 CST)
    - Re: GPU acceleration by using ATI video card Aron Broom (Fri Dec 14 2012 - 03:13:40 CST)
    - Re: GPU acceleration by using ATI video card dongsheng lei (Fri Dec 14 2012 - 03:42:08 CST)
- Re: GPU acceleration by using ATI video card Axel Kohlmeyer (Fri Dec 14 2012 - 03:11:06 CST)
understanding the energy term in NAMD log file ç¿æž—å²½ (Wed Dec 12 2012 - 20:46:31 CST)
- Re: understanding the energy term in NAMD log file Jeffrey Potoff (Wed Dec 12 2012 - 21:46:16 CST)
checkpoint and revert Dr. Eddie (Wed Dec 12 2012 - 15:04:14 CST)
Alchemical transformations and DDG of point mutations Gianluca Interlandi (Wed Dec 12 2012 - 14:22:55 CST)
- Re: Alchemical transformations and DDG of point mutations Chris Chipot (Wed Dec 12 2012 - 15:02:02 CST)
  - Re: Alchemical transformations and DDG of point mutations Gianluca Interlandi (Wed Dec 12 2012 - 16:24:09 CST)
Multicore executable error with hydrogens Caitlin Scott (Tue Dec 11 2012 - 20:55:36 CST)
weird energy values of LJ fluids Lindong Weng (Tue Dec 11 2012 - 16:15:55 CST)
Alchemical transformations and DDG of point mutations Gianluca Interlandi (Tue Dec 11 2012 - 15:22:37 CST)
- NAMD and new FF CHARMM36 Gianluca Interlandi (Wed Dec 12 2012 - 14:26:07 CST)
  - Re: NAMD and new FF CHARMM36 Evgeny Bulat (Wed Dec 12 2012 - 14:39:48 CST)
    - Re: NAMD and new FF CHARMM36 Gianluca Interlandi (Wed Dec 12 2012 - 14:49:46 CST)
    - Re: NAMD and new FF CHARMM36 Jeffrey Potoff (Wed Dec 12 2012 - 15:22:03 CST)
  - Re: NAMD and new FF CHARMM36 JC Gumbart (Wed Dec 12 2012 - 14:53:19 CST)
    - Re: NAMD and new FF CHARMM36 Evgeny Bulat (Wed Dec 12 2012 - 15:24:58 CST)
Weird energy values of LJ fluids simulation Lindong Weng (Tue Dec 11 2012 - 13:43:16 CST)
REST or RESTMD in NAMD? Gareth Shannon (Tue Dec 11 2012 - 12:08:21 CST)
- Re: REST or RESTMD in NAMD? francesco oteri (Tue Dec 11 2012 - 12:22:47 CST)
TAU profiler with NAMD2.9 smp mode Takuro Udagawa (Tue Dec 11 2012 - 07:44:44 CST)
convergence of FEP calculation. dbaogen (Mon Dec 10 2012 - 21:16:09 CST)
Colvars value is out of boundary DAI, JIAN (Mon Dec 10 2012 - 16:15:45 CST)
- Re: Colvars value is out of boundary Aron Broom (Mon Dec 10 2012 - 16:29:18 CST)
- Re: Colvars value is out of boundary Giacomo Fiorin (Mon Dec 10 2012 - 16:29:52 CST)
error in psf file farzad kiani (Mon Dec 10 2012 - 09:47:00 CST)
FEP simulation using AmberFF Jiyong Park (Mon Dec 10 2012 - 01:41:28 CST)
minimization, slow heating and then Langevin free runs Dr. Eddie (Sun Dec 09 2012 - 10:16:21 CST)
- Re: minimization, slow heating and then Langevin free runs Rajan Vatassery (Sun Dec 09 2012 - 17:02:10 CST)
  - Re: minimization, slow heating and then Langevin free runs Dr. Eddie (Mon Dec 10 2012 - 09:08:05 CST)
  - Re: minimization, slow heating and then Langevin free runs Rajan Vatassery (Fri Dec 14 2012 - 13:38:02 CST)
Getting "nan" at ELEC energy value jesmin jahan (Fri Dec 07 2012 - 22:48:46 CST)
- Re: Getting "nan" at ELEC energy value Aron Broom (Sat Dec 08 2012 - 00:22:13 CST)
NAMD CUDA 2.9 Performance drop compared to 2.8 Norman Geist (Fri Dec 07 2012 - 05:37:20 CST)
ask for new toppar files for drude in NAMD2.9 Huihui Liu (Thu Dec 06 2012 - 05:30:25 CST)
aMD with implicit solvent - Segmentation fault Thomas Evangelidis (Wed Dec 05 2012 - 10:43:57 CST)
Simulation Box Deformation John Doe (Mon Dec 03 2012 - 20:19:47 CST)
how to find cellorigin for periodic boundary condition Maria Saeed (Tue Dec 04 2012 - 10:34:09 CST)
- how to find cellorigin for periodic boundary condition Maria Saeed (Tue Dec 04 2012 - 10:35:39 CST)
- Re: how to find cellorigin for periodic boundary condition Axel Kohlmeyer (Tue Dec 04 2012 - 10:37:47 CST)
NAMD parameters +mergegrids +ignoresharing Norman Geist (Tue Dec 04 2012 - 01:04:09 CST)
How to compute "only the GB Energy" using NAMD? jesmin jahan (Mon Dec 03 2012 - 20:34:02 CST)
- Re: How to compute "only the GB Energy" using NAMD? jesmin jahan (Wed Dec 05 2012 - 09:52:15 CST)
  - Re: How to compute "only the GB Energy" using NAMD? David Minh (Wed Dec 05 2012 - 09:56:09 CST)
    - Re: How to compute "only the GB Energy" using NAMD? jesmin jahan (Thu Dec 06 2012 - 07:44:43 CST)
What's the difference between upperboundary and upperwall? DAI, JIAN (Mon Dec 03 2012 - 16:34:32 CST)
- Re: What's the difference between upperboundary and upperwall? Giacomo Fiorin (Mon Dec 03 2012 - 16:38:07 CST)
Simulation Box Deformation John Doe (Mon Dec 03 2012 - 15:51:57 CST)
- AW: Simulation Box Deformation Norman Geist (Tue Dec 04 2012 - 00:57:13 CST)
  - RE: AW: Simulation Box Deformation John Doe (Tue Dec 04 2012 - 06:24:09 CST)
    - Re: AW: Simulation Box Deformation Axel Kohlmeyer (Tue Dec 04 2012 - 11:40:26 CST)
problems with simulation of LJ fluid ç¿æž—å²½ (Sat Dec 01 2012 - 17:30:28 CST)
- Re: problems with simulation of LJ fluid Axel Kohlmeyer (Mon Dec 03 2012 - 11:20:58 CST)
  - Re: problems with simulation of LJ fluid Jeffrey Potoff (Mon Dec 03 2012 - 12:09:01 CST)
- Re: problems with simulation of LJ fluid Rajan Vatassery (Mon Dec 03 2012 - 12:35:42 CST)
about long namd trajectory and pbc effect Liqun Zhang (Sun Dec 02 2012 - 14:53:24 CST)
- Re: about long namd trajectory and pbc effect Thomas Evangelidis (Sun Dec 02 2012 - 15:39:36 CST)
  - AW: about long namd trajectory and pbc effect Norman Geist (Mon Dec 03 2012 - 00:44:31 CST)
  - Re: about long namd trajectory and pbc effect Liqun Zhang (Mon Dec 03 2012 - 14:00:50 CST)
namd runs on compute nodes but not update files in the head node Ada Zhan (Fri Nov 30 2012 - 16:34:01 CST)
Re: NAMD parameters +mergegrids +ignoresharing Aron Broom (Fri Nov 30 2012 - 09:41:04 CST)
Force field Parametrization Dr. Eddie (Fri Nov 30 2012 - 09:09:34 CST)
- Re: Force field Parametrization Thomas Evangelidis (Fri Nov 30 2012 - 09:39:49 CST)
- RE: Force field Parametrization JC Gumbart (Fri Nov 30 2012 - 10:34:05 CST)
NAMD parameters +mergegrids +ignoresharing Norman Geist (Fri Nov 30 2012 - 00:49:17 CST)
AccelMD + GBIS Felipe Merino (Thu Nov 29 2012 - 09:39:18 CST)
- Re: AccelMD + GBIS Jeff Wereszczynski (Thu Nov 29 2012 - 16:57:24 CST)
  - Re: AccelMD + GBIS Felipe Merino (Fri Nov 30 2012 - 04:26:21 CST)
Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS Tristan Croll (Wed Nov 28 2012 - 05:40:18 CST)
- Re: Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS Aron Broom (Thu Nov 29 2012 - 17:01:23 CST)
  - AW: Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS Norman Geist (Fri Nov 30 2012 - 00:32:14 CST)
  - RE: Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS Tristan Croll (Thu Nov 29 2012 - 17:42:53 CST)
performance variation during run time Thomas C. Bishop (Wed Nov 28 2012 - 18:53:10 CST)
- AW: performance variation during run time Norman Geist (Thu Nov 29 2012 - 01:26:31 CST)
error Maria Saeed (Wed Nov 28 2012 - 03:24:50 CST)
- Re: error Axel Kohlmeyer (Wed Nov 28 2012 - 03:29:35 CST)
error regarding membrane embedded protein Maria Saeed (Wed Nov 28 2012 - 01:58:31 CST)
- Re: error regarding membrane embedded protein Axel Kohlmeyer (Wed Nov 28 2012 - 02:23:21 CST)
performance loss on GPUs Thomas Evangelidis (Wed Nov 28 2012 - 01:13:53 CST)
- Re: performance loss on GPUs Aron Broom (Wed Nov 28 2012 - 01:31:12 CST)
- Re: performance loss on GPUs Axel Kohlmeyer (Wed Nov 28 2012 - 02:21:14 CST)
  - Re: performance loss on GPUs Aron Broom (Wed Nov 28 2012 - 09:57:06 CST)
Should the windows for ABF calculations be overlapped or not? DAI, JIAN (Tue Nov 27 2012 - 08:38:17 CST)
- RE: Should the windows for ABF calculations be overlapped or not? JC Gumbart (Tue Nov 27 2012 - 09:12:48 CST)
Re: how to run NAMD-CUDA on multiple nodes Thomas Evangelidis (Tue Nov 27 2012 - 03:20:16 CST)
- AW: how to run NAMD-CUDA on multiple nodes Norman Geist (Tue Nov 27 2012 - 08:57:08 CST)
- Re: how to run NAMD-CUDA on multiple nodes Thomas Evangelidis (Tue Nov 27 2012 - 10:13:07 CST)
  - AW: how to run NAMD-CUDA on multiple nodes Norman Geist (Wed Nov 28 2012 - 01:29:58 CST)
- Re: how to run NAMD-CUDA on multiple nodes Thomas Evangelidis (Wed Nov 28 2012 - 01:45:14 CST)
  - AW: how to run NAMD-CUDA on multiple nodes Norman Geist (Wed Nov 28 2012 - 03:45:53 CST)
Functionalizing the nanopore Sridhar Kumar Kannam (Mon Nov 26 2012 - 23:24:19 CST)
how to run NAMD-CUDA on multiple nodes Thomas Evangelidis (Mon Nov 26 2012 - 07:57:18 CST)
- AW: how to run NAMD-CUDA on multiple nodes Norman Geist (Tue Nov 27 2012 - 02:09:01 CST)
AW: AW: AW: libcudart.so.4 error Norman Geist (Mon Nov 26 2012 - 00:11:25 CST)
Replica exchange - Temperatures and number of replicas Siri Søndergaard (Sun Nov 25 2012 - 17:06:44 CST)
- Re: Replica exchange - Temperatures and number of replicas Aron Broom (Sun Nov 25 2012 - 19:27:42 CST)
Benchmarks for GTX 690's and 590's Dr. Eddie (Sun Nov 25 2012 - 11:41:46 CST)
- Re: Benchmarks for GTX 690's and 590's Aron Broom (Sun Nov 25 2012 - 13:25:19 CST)
  - Re: Benchmarks for GTX 690's and 590's Dr. Eddie (Sun Nov 25 2012 - 20:11:47 CST)
    - Re: Benchmarks for GTX 690's and 590's Dr. Eddie (Wed Nov 28 2012 - 09:12:12 CST)
    - AW: Benchmarks for GTX 690's and 590's Norman Geist (Wed Nov 28 2012 - 10:04:50 CST)
  - Re: Benchmarks for GTX 690's and 590's Axel Kohlmeyer (Wed Nov 28 2012 - 10:11:27 CST)
    - Re: Benchmarks for GTX 690's and 590's Dr. Eddie (Wed Nov 28 2012 - 10:35:53 CST)
question about relative binding free energy calculation method using FEP dbaogen (Sat Nov 24 2012 - 05:58:55 CST)
- Re: question about relative binding free energy calculation method using FEP Chris Chipot (Sat Nov 24 2012 - 09:54:46 CST)
  - å›žå¤: Re: question about relative binding free energy calculation method using FEP dbaogen (Sat Nov 24 2012 - 21:50:05 CST)
    - Re: å›žå¤: Re: question about relative binding free energy calculation method using FEP JC Gumbart (Sun Nov 25 2012 - 00:46:48 CST)
(no subject) Steven W Rick (Fri Nov 23 2012 - 14:29:17 CST)
- Re: Axel Kohlmeyer (Sat Nov 24 2012 - 06:17:07 CST)
libcudart.so.4 error flavio seixas (Thu Nov 22 2012 - 12:42:57 CST)
- Re: libcudart.so.4 error Aron Broom (Thu Nov 22 2012 - 13:25:23 CST)
  - Re: libcudart.so.4 error Thomas Evangelidis (Thu Nov 22 2012 - 13:50:18 CST)
  - Re: libcudart.so.4 error flavio seixas (Thu Nov 22 2012 - 13:57:53 CST)
NAMD 2.9 not migrating to computing nodes on Windows Server 2008 R2 HPC MPI Alex Smith (Thu Nov 22 2012 - 05:44:28 CST)
NAMDEnergy: run with XSC file or not? Evgeny Bulat (Wed Nov 21 2012 - 13:27:23 CST)
- AW: NAMDEnergy: run with XSC file or not? Norman Geist (Thu Nov 22 2012 - 00:43:49 CST)
- AW: NAMDEnergy: run with XSC file or not? Norman Geist (Thu Nov 22 2012 - 00:40:21 CST)
src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target Paraskevi Gkeka (Wed Nov 21 2012 - 06:14:09 CST)
Re: namd-l digest V1 #918 Aaron Cann (Tue Nov 20 2012 - 13:10:24 CST)
Parametarization and geometry optimization Dhiraj Srivastava (Tue Nov 20 2012 - 07:26:35 CST)
- RE: Parametarization and geometry optimization. . Martin, Erik W (Tue Nov 20 2012 - 08:14:11 CST)
  - Re: Parametarization and geometry optimization. . Ajasja LjubetiÄ (Tue Nov 20 2012 - 08:25:34 CST)
problem in accelerated MD with NAMD-GPU Thomas Evangelidis (Mon Nov 19 2012 - 11:19:56 CST)
ABACAVIR parameters Athanassios Stavrakoudis (Mon Nov 19 2012 - 08:38:12 CST)
where does the second boost in accelMDdual mode refer to Thomas Evangelidis (Sun Nov 18 2012 - 16:25:50 CST)
Compiling NAMD with CUDA on MacOSX Mountain Lion Maximilian Ebert (Sat Nov 17 2012 - 18:39:25 CST)
Compiling NAMD with CUDA on MacOSX Mountain Lion Maximilian Ebert (Sat Nov 17 2012 - 18:38:51 CST)
pressure profile calculations upayan baul (Sat Nov 17 2012 - 04:55:59 CST)
Re: NAMD failed to read AMBER parm file Sneha Menon (Sat Nov 17 2012 - 03:44:08 CST)
- Re: NAMD failed to read AMBER parm file Felipe Merino (Sat Nov 17 2012 - 10:48:12 CST)
cross terms Dr. Eddie (Fri Nov 16 2012 - 13:15:59 CST)
- Re: cross terms JC Gumbart (Fri Nov 16 2012 - 13:48:37 CST)
  - Re: cross terms Dr. Eddie (Fri Nov 16 2012 - 13:51:19 CST)
    - Re: cross terms JC Gumbart (Fri Nov 16 2012 - 14:26:56 CST)
  - Re: cross terms JC Gumbart (Sat Nov 17 2012 - 16:24:49 CST)
(no subject) saman amiri (Fri Nov 16 2012 - 08:05:21 CST)
Conflict between CUDA NAMD and PMEMD Martin, Erik W (Thu Nov 15 2012 - 18:38:55 CST)
Carma v.1.2 released. Nicholas M Glykos (Thu Nov 15 2012 - 04:22:25 CST)
How to decide whether an ABF curve has been converged? dream (Thu Nov 15 2012 - 03:38:39 CST)
- Re: How to decide whether an ABF curve has been converged? Jérôme Hénin (Thu Nov 15 2012 - 04:50:00 CST)
  - Re: How to decide whether an ABF curve has been converged? Aron Broom (Thu Nov 15 2012 - 14:52:48 CST)
acylated and amidated parameters. Martin, Erik W (Wed Nov 14 2012 - 11:45:32 CST)
- Re: acylated and amidated parameters. JC Gumbart (Wed Nov 14 2012 - 17:20:55 CST)
Force Field Topology and Parameter Files Stephen Holmes (Tue Nov 13 2012 - 09:00:59 CST)
- AW: Force Field Topology and Parameter Files Norman Geist (Wed Nov 14 2012 - 00:15:42 CST)
Replica-exchange metadynamics scripts Robert Elder (Tue Nov 13 2012 - 12:12:39 CST)
- Re: Replica-exchange metadynamics scripts Aron Broom (Sat Nov 17 2012 - 10:52:33 CST)
  - Re: Replica-exchange metadynamics scripts Robert Elder (Thu Feb 14 2013 - 18:29:53 CST)
Re: Bond Breaking in Polymer Networks - United Atom Forcefield Axel Kohlmeyer (Tue Nov 13 2012 - 10:53:11 CST)
Errors compiling namd with CUDA Martin, Erik W (Tue Nov 13 2012 - 10:15:53 CST)
- RE: Errors compiling namd with CUDA. . Martin, Erik W (Tue Nov 13 2012 - 17:43:50 CST)
metadynamics/ABF simulations using collective variables - issues with restarting the calculations Marimuthu Krishnan (Tue Nov 13 2012 - 08:42:43 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Jérôme Hénin (Tue Nov 13 2012 - 10:21:19 CST)
  - Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Aron Broom (Tue Nov 13 2012 - 10:47:52 CST)
  - Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Marimuthu Krishnan (Tue Nov 13 2012 - 13:22:57 CST)
Bond Breaking in Polymer Networks - United Atom Forcefield Stefanos Anogiannakis (Tue Nov 13 2012 - 04:14:38 CST)
- AW: Bond Breaking in Polymer Networks - United Atom Forcefield Norman Geist (Tue Nov 13 2012 - 10:40:42 CST)
Replica-exchange MD on a single node / SMP workstation Zachary Ulissi (Fri Nov 09 2012 - 17:57:26 CST)
- AW: Replica-exchange MD on a single node / SMP workstation Norman Geist (Mon Nov 12 2012 - 00:33:23 CST)
Information about error compiling with CUDA Martin, Erik W (Fri Nov 09 2012 - 14:50:44 CST)
create junction between nanotubes farzad kiani (Fri Nov 09 2012 - 06:13:59 CST)
NAMD failed to read AMBER parm file Sneha Menon (Thu Nov 08 2012 - 23:19:00 CST)
- AW: NAMD failed to read AMBER parm file Norman Geist (Fri Nov 09 2012 - 01:37:25 CST)
Re: CUDA error vs clashes Francesco Pietra (Thu Nov 08 2012 - 11:42:09 CST)
- Re: CUDA error vs clashes Francesco Pietra (Fri Nov 09 2012 - 01:52:32 CST)
Moving atoms with bad contacts followed by CUDA error Francesco Pietra (Thu Nov 08 2012 - 09:45:00 CST)
A bug in replica.namd? Ada Zhan (Wed Nov 07 2012 - 16:37:13 CST)
- RE: A bug in replica.namd? Ada Zhan (Thu Nov 08 2012 - 13:32:39 CST)
Input configuration files for GPU version of NAMD Ganesh Kamath (Wed Nov 07 2012 - 12:56:27 CST)
- Re: Input configuration files for GPU version of NAMD Axel Kohlmeyer (Wed Nov 07 2012 - 13:03:22 CST)
Accelerated MD Felipe Merino (Wed Nov 07 2012 - 10:08:15 CST)
Fwd: CUDA error vs clashes Francesco Pietra (Wed Nov 07 2012 - 09:26:19 CST)
CUDA error (as a misleding error message) Francesco Pietra (Wed Nov 07 2012 - 05:33:41 CST)
- Re: CUDA error (as a misleding error message) Aron Broom (Wed Nov 07 2012 - 10:01:51 CST)
replica exchange and replica.namd Siri Søndergaard (Tue Nov 06 2012 - 20:57:18 CST)
no. of CPUs for optimal GTX-690 performance Michael Purdy (Tue Nov 06 2012 - 13:01:41 CST)
- Re: no. of CPUs for optimal GTX-690 performance Ajasja LjubetiÄ (Tue Nov 06 2012 - 13:43:28 CST)
  - Re: no. of CPUs for optimal GTX-690 performance Aron Broom (Wed Nov 07 2012 - 02:16:46 CST)
    - Re: no. of CPUs for optimal GTX-690 performance Axel Kohlmeyer (Wed Nov 07 2012 - 02:45:29 CST)
- Re: no. of CPUs for optimal GTX-690 performance Aron Broom (Tue Nov 06 2012 - 13:44:06 CST)
- Re: no. of CPUs for optimal GTX-690 performance Giacomo Fiorin (Tue Nov 06 2012 - 14:46:02 CST)
  - AW: no. of CPUs for optimal GTX-690 performance Norman Geist (Wed Nov 07 2012 - 01:56:25 CST)
  - Re: no. of CPUs for optimal GTX-690 performance Ajasja LjubetiÄ (Wed Nov 07 2012 - 04:34:10 CST)
namd 2.9 Replica Exchange with colvar Ada Zhan (Mon Nov 05 2012 - 13:11:30 CST)
Re: increment torsion restrain before minimization Tina Stokelj (Mon Nov 05 2012 - 06:38:32 CST)
- Re: increment torsion restrain before minimization Tina Stokelj (Mon Nov 05 2012 - 07:16:59 CST)
  - Re: increment torsion restrain before minimization Axel Kohlmeyer (Mon Nov 05 2012 - 07:53:39 CST)
Re: NAMD 2.9 Windows CUDA build? Axel Kohlmeyer (Mon Nov 05 2012 - 02:01:30 CST)
increment torsion restrain before minimization Tina Stokelj (Sat Nov 03 2012 - 09:59:43 CDT)
- AW: increment torsion restrain before minimization Norman Geist (Mon Nov 05 2012 - 01:32:39 CST)
- Re: increment torsion restrain before minimization Ajasja LjubetiÄ (Mon Nov 05 2012 - 07:35:19 CST)
NAMD 2.9 Windows CUDA build? Frederik Heurlin Aidt (Fri Nov 02 2012 - 05:30:54 CDT)
- AW: NAMD 2.9 Windows CUDA build? Norman Geist (Mon Nov 05 2012 - 01:27:43 CST)
- RE: NAMD 2.9 Windows CUDA build? Frederik Heurlin Aidt (Thu Nov 08 2012 - 02:51:33 CST)
  - Re: RE: NAMD 2.9 Windows CUDA build? Ajasja LjubetiÄ (Thu Nov 08 2012 - 03:47:01 CST)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG2R Shubhra Ghosh Dastidar (Wed Oct 31 2012 - 21:55:49 CDT)
malloc memory error using CUDA devices Blake Mertz (Wed Oct 31 2012 - 07:25:11 CDT)
- AW: malloc memory error using CUDA devices Norman Geist (Thu Nov 01 2012 - 02:01:50 CDT)
namd 2.9 and plumed Vlad Cojocaru (Wed Oct 31 2012 - 07:24:07 CDT)
Metadynamics and Colvar Width Marc Gordon (Mon Oct 29 2012 - 09:19:45 CDT)
- Re: Metadynamics and Colvar Width Aron Broom (Mon Oct 29 2012 - 12:53:22 CDT)
compilation with CUDA error Thomas Evangelidis (Mon Oct 29 2012 - 08:44:23 CDT)
- Re: compilation with CUDA error Aron Broom (Mon Oct 29 2012 - 12:43:44 CDT)
  - AW: compilation with CUDA error Norman Geist (Tue Oct 30 2012 - 02:19:22 CDT)
  - Re: compilation with CUDA error Thomas Evangelidis (Tue Oct 30 2012 - 02:59:41 CDT)
Colvars Error? David Minh (Fri Oct 26 2012 - 11:13:21 CDT)
- Re: Colvars Error? Giacomo Fiorin (Fri Oct 26 2012 - 12:56:33 CDT)
  - Re: Colvars Error? David Minh (Fri Oct 26 2012 - 13:20:21 CDT)
    - Re: Colvars Error? JC Gumbart (Fri Oct 26 2012 - 21:26:42 CDT)
    - Re: Colvars Error? David Minh (Fri Oct 26 2012 - 22:02:12 CDT)
SMD: Compressing a Molecule raghav singh (Thu Oct 25 2012 - 14:57:32 CDT)
Restarting Multiple Walker/Well Tempered Metadynamics Jeff Wereszczynski (Thu Oct 25 2012 - 13:17:27 CDT)
- Re: Restarting Multiple Walker/Well Tempered Metadynamics Giacomo Fiorin (Thu Oct 25 2012 - 16:18:49 CDT)
NAMD compilation -- compiler issue Dmitry Osolodkin (Thu Oct 25 2012 - 09:02:22 CDT)
- Re: NAMD compilation -- compiler issue Sergey (Thu Oct 25 2012 - 09:46:10 CDT)
  - Re: NAMD compilation -- compiler issue Dmitry Osolodkin (Fri Oct 26 2012 - 03:33:15 CDT)
unreasonably high temp/pressure Martin, Erik W (Wed Oct 24 2012 - 09:55:52 CDT)
- Re: unreasonably high temp/pressure Aron Broom (Wed Oct 24 2012 - 10:26:43 CDT)
  - Re: unreasonably high temp/pressure Martin, Erik W (Wed Oct 24 2012 - 10:34:57 CDT)
    - Re: unreasonably high temp/pressure Aron Broom (Wed Oct 24 2012 - 12:56:36 CDT)
    - Re: unreasonably high temp/pressure Martin, Erik W (Wed Oct 24 2012 - 14:33:41 CDT)
  - Re: unreasonably high temp/pressure Jesper Sørensen (Wed Oct 24 2012 - 15:00:07 CDT)
CUDA - OwnerBox::close failure Vlastimil ZÃma (Wed Oct 24 2012 - 05:21:43 CDT)
AW: How can I write a log file on my cluster? Norman Geist (Wed Oct 24 2012 - 00:42:06 CDT)
Hybrid Monte Carlo? David Minh (Tue Oct 23 2012 - 09:58:26 CDT)
Grid Forces: example code, documentation edit, and requested feature David Minh (Tue Oct 23 2012 - 09:49:26 CDT)
extract velocities Giulia (Tue Oct 23 2012 - 06:58:38 CDT)
- AW: extract velocities Norman Geist (Wed Oct 24 2012 - 00:34:56 CDT)
Pressure problem to equilibrate NPT Mariana Graterol (Mon Oct 22 2012 - 17:28:55 CDT)
- Re: Pressure problem to equilibrate NPT Aron Broom (Mon Oct 22 2012 - 21:14:42 CDT)
How can I write a log file on my cluster? äÍÉÔÒÉÊ âÅÇÏ×ÁÔÏ× (Mon Oct 22 2012 - 01:39:58 CDT)
- AW: How can I write a log file on my cluster? Norman Geist (Mon Oct 22 2012 - 09:04:29 CDT)
  - AW: How can I write a log file on my cluster? Norman Geist (Tue Oct 23 2012 - 00:30:44 CDT)
inputPrefix for ABF Branko (Sat Oct 20 2012 - 16:36:16 CDT)
- Re: inputPrefix for ABF Giacomo Fiorin (Sun Oct 21 2012 - 13:43:52 CDT)
  - solved inputPrefix for ABF Branko (Sun Oct 21 2012 - 15:24:43 CDT)
NAMD (and VMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags) Jose Borreguero (Sat Oct 20 2012 - 15:55:51 CDT)
- Re: NAMD (and VMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags) Aron Broom (Sun Oct 21 2012 - 18:37:56 CDT)
NAMD in parallel on CPUs of different type Thomas Albers (Fri Oct 19 2012 - 21:03:08 CDT)
- Re: NAMD in parallel on CPUs of different type Chris Harrison (Fri Oct 19 2012 - 21:29:05 CDT)
  - Re: NAMD in parallel on CPUs of different type Thomas Albers (Fri Oct 19 2012 - 21:51:47 CDT)
REMD and NAMD options Martin, Erik W (Fri Oct 19 2012 - 09:36:38 CDT)
optimal CPU number for parallel MD of a small system Isaure Chauvot de Beauchêne (Fri Oct 19 2012 - 08:32:57 CDT)
- Re: optimal CPU number for parallel MD of a small system Mert Gür (Fri Oct 19 2012 - 08:49:43 CDT)
Re: NAMD SGE Job Script Scale Up issues! Aditya Ranganathan (Fri Oct 19 2012 - 02:29:07 CDT)
duplicate residue key Katrin Stöbener (Fri Oct 19 2012 - 02:30:19 CDT)
Pressure in equilibration stage of MD Mariana Graterol (Thu Oct 18 2012 - 16:52:05 CDT)
- Re: Pressure in equilibration stage of MD Aron Broom (Thu Oct 18 2012 - 17:34:02 CDT)
  - Re: Pressure in equilibration stage of MD Mariana Graterol (Fri Oct 19 2012 - 08:42:24 CDT)
NAMD SGE Job Script Scale Up issues! Aditya Ranganathan (Thu Oct 18 2012 - 08:04:53 CDT)
- AW: NAMD SGE Job Script Scale Up issues! Norman Geist (Fri Oct 19 2012 - 00:41:54 CDT)
Invitation to connect on LinkedIn Adebayo Adeleke via LinkedIn (Wed Oct 17 2012 - 03:28:28 CDT)
the fictitious force or the viscosity of water ishiikai08_at_yahoo.co.jp (Wed Oct 17 2012 - 02:44:04 CDT)
1-4 tabulated potentials? Jorge Hernandez Cobos (Tue Oct 16 2012 - 15:04:57 CDT)
pulling constant verocity ishiikai08_at_yahoo.co.jp (Tue Oct 16 2012 - 02:13:22 CDT)
postdoc position available JC Gumbart (Tue Oct 16 2012 - 00:47:41 CDT)
compiling namd-2.9 on bluegeneQ Zhuyi Xue (Mon Oct 15 2012 - 15:46:40 CDT)
Vacuum simulations mohan maruthi sena (Mon Oct 15 2012 - 14:16:04 CDT)
- Re: Vacuum simulations Aron Broom (Mon Oct 15 2012 - 15:14:28 CDT)
Handling torsional potentials other than CHARMM type - regd Ramesh Cheerla (Fri Oct 12 2012 - 14:46:10 CDT)
- Re: Handling torsional potentials other than CHARMM type - regd Jeffrey Potoff (Fri Oct 12 2012 - 15:34:01 CDT)
question of MMPBSA calculation combined NAMD and APBS software baogen duan (Thu Oct 11 2012 - 20:52:22 CDT)
- Re: question of MMPBSA calculation combined NAMD and APBS software Aron Broom (Thu Oct 11 2012 - 22:18:13 CDT)
help with how pbc are defined. Martin, Erik W (Thu Oct 11 2012 - 12:48:27 CDT)
- Re: help with how pbc are defined. David Hardy (Thu Oct 11 2012 - 13:34:10 CDT)
  - Re: help with how pbc are defined.. . Martin, Erik W (Fri Oct 12 2012 - 09:39:34 CDT)
    - Re: help with how pbc are defined.. . David Hardy (Fri Oct 12 2012 - 12:16:14 CDT)
Basic question on fixed atom Ganesh Kamath (Thu Oct 11 2012 - 09:08:37 CDT)
structure changing ishiikai08_at_yahoo.co.jp (Wed Oct 10 2012 - 23:51:12 CDT)
- Re: structure changing Aron Broom (Thu Oct 11 2012 - 06:33:53 CDT)
Tabulated potentials - regd Ramesh Cheerla (Tue Oct 09 2012 - 09:01:52 CDT)
- Re: Tabulated potentials - regd Jérôme Hénin (Tue Oct 09 2012 - 11:29:47 CDT)
Warning & error Narasimhan LOGANATHAN (Tue Oct 09 2012 - 08:48:43 CDT)
- Re: Warning & error Narasimhan LOGANATHAN (Wed Oct 10 2012 - 05:07:54 CDT)
velocity distribution Namd Namd (Mon Oct 08 2012 - 06:46:52 CDT)
- Re: velocity distribution David Hardy (Mon Oct 08 2012 - 12:54:52 CDT)
units of pmf files Marc Gordon (Mon Oct 08 2012 - 05:42:37 CDT)
- Re: units of pmf files Jérôme Hénin (Mon Oct 08 2012 - 06:12:51 CDT)
Fixed atoms in SMD khalil ghafarian (Mon Oct 08 2012 - 05:22:25 CDT)
- Re: Fixed atoms in SMD Axel Kohlmeyer (Mon Oct 08 2012 - 07:00:09 CDT)
  - Re: Fixed atoms in SMD khalil ghafarian (Tue Oct 09 2012 - 03:40:20 CDT)
Running fulldirect in parallel Tom Coles (Sun Oct 07 2012 - 15:08:11 CDT)
- Re: Running fulldirect in parallel Aron Broom (Sun Oct 07 2012 - 15:14:10 CDT)
  - RE: Running fulldirect in parallel Tom Coles (Sun Oct 07 2012 - 15:21:32 CDT)
    - Re: Running fulldirect in parallel Aron Broom (Sun Oct 07 2012 - 15:43:54 CDT)
a question on version nightly build flatforms Hyonseok Hwang (Sun Oct 07 2012 - 01:26:26 CDT)
tcl script for rmsd yp sun (Thu Oct 04 2012 - 04:43:37 CDT)
- Re: tcl script for rmsd Aron Broom (Thu Oct 04 2012 - 11:18:29 CDT)
release the memory taking by the aotmselects/vars Jacqueline Schmidt (Wed Oct 03 2012 - 10:45:48 CDT)
box dimension for unwrapped boxes? Jacqueline Schmidt (Wed Oct 03 2012 - 10:14:09 CDT)
- Re: box dimension for unwrapped boxes? Aron Broom (Wed Oct 03 2012 - 10:19:05 CDT)
  - Re: box dimension for unwrapped boxes? Jacqueline Schmidt (Wed Oct 03 2012 - 10:32:37 CDT)
    - AW: box dimension for unwrapped boxes? Norman Geist (Thu Oct 04 2012 - 01:05:47 CDT)
Cuda errors in Ubuntu12amd64 ´ÞÓ×Ìñ (Tue Oct 02 2012 - 22:33:49 CDT)
- AW: Cuda errors in Ubuntu12amd64 Norman Geist (Thu Oct 04 2012 - 00:51:13 CDT)
Is the TMD equation in the user manual correct? Mert Gür (Tue Oct 02 2012 - 12:43:00 CDT)
- Re: Is the TMD equation in the user manual correct? JC Gumbart (Fri Oct 05 2012 - 13:26:56 CDT)
  - Re: Is the TMD equation in the user manual correct? Mert Gür (Fri Oct 05 2012 - 15:01:03 CDT)
    - Re: Is the TMD equation in the user manual correct? JC Gumbart (Fri Oct 05 2012 - 15:47:39 CDT)
    - Re: Is the TMD equation in the user manual correct? Jérôme Hénin (Mon Oct 08 2012 - 07:10:57 CDT)
handling buckingham potentials in NAMD - regd Ramesh Cheerla (Tue Oct 02 2012 - 10:17:47 CDT)
expandBoundaries and multiple walker metadynamics Jeff Wereszczynski (Mon Oct 01 2012 - 13:52:53 CDT)
- Re: expandBoundaries and multiple walker metadynamics Giacomo Fiorin (Mon Oct 01 2012 - 14:21:11 CDT)
  - Re: expandBoundaries and multiple walker metadynamics Jeff Wereszczynski (Mon Oct 01 2012 - 14:52:08 CDT)
intergation algoritm of NAMD Namd Namd (Mon Oct 01 2012 - 03:52:30 CDT)
Convergence of the Gram-Charlier expansion Ali Khanlarkhani (Sun Sep 30 2012 - 10:34:56 CDT)
- Re: Convergence of the Gram-Charlier expansion Chris Chipot (Sun Sep 30 2012 - 11:46:58 CDT)
  - Re: Convergence of the Gram-Charlier expansion Ali Khanlarkhani (Sun Sep 30 2012 - 12:32:29 CDT)
Umbrella Sampling after multiple replicas metadynamics Aron Broom (Fri Sep 28 2012 - 16:23:15 CDT)
- Re: Umbrella Sampling after multiple replicas metadynamics Giacomo Fiorin (Fri Sep 28 2012 - 16:33:54 CDT)
  - Re: Umbrella Sampling after multiple replicas metadynamics Aron Broom (Fri Sep 28 2012 - 16:53:09 CDT)
Namd list: Problem in equilibration stage Mariana Graterol (Thu Sep 27 2012 - 08:35:31 CDT)
- Re: Namd list: Problem in equilibration stage Aron Broom (Thu Sep 27 2012 - 11:31:18 CDT)
experimental density value oguz gurbulak (Thu Sep 27 2012 - 07:40:35 CDT)
- Re: experimental density value Guanglei Cui (Thu Sep 27 2012 - 14:17:47 CDT)
  - Re: experimental density value Aron Broom (Thu Sep 27 2012 - 20:13:04 CDT)
    - Re: experimental density value Ganesh Kamath (Thu Sep 27 2012 - 20:52:16 CDT)
Re: compiling charm++ Error: can not find mpi library Thomas Evangelidis (Thu Sep 27 2012 - 02:00:24 CDT)
- AW: compiling charm++ Error: can not find mpi library Norman Geist (Thu Sep 27 2012 - 08:14:57 CDT)
- Re: compiling charm++ Error: can not find mpi library Thomas Evangelidis (Thu Sep 27 2012 - 08:24:57 CDT)
compiling charm++ Error: can not find mpi library Thomas Evangelidis (Wed Sep 26 2012 - 17:15:00 CDT)
- AW: compiling charm++ Error: can not find mpi library Norman Geist (Thu Sep 27 2012 - 01:46:23 CDT)
Parameters for 3 methyl histidine. amin_at_imtech.res.in (Wed Sep 26 2012 - 09:13:34 CDT)
namd on nvidia 302.17 Francesco Pietra (Wed Sep 26 2012 - 08:58:45 CDT)
- Re: namd on nvidia 302.17 Aron Broom (Wed Sep 26 2012 - 09:05:07 CDT)
  - Re: namd on nvidia 302.17 Francesco Pietra (Thu Sep 27 2012 - 02:52:11 CDT)
Re: W and S Axel Kohlmeyer (Tue Sep 25 2012 - 12:45:40 CDT)
W and S Mikhail Suyetin (Tue Sep 25 2012 - 05:24:34 CDT)
Printing energy of selected atoms in NAMD Ganesh Kamath (Mon Sep 24 2012 - 13:59:33 CDT)
- Re: Printing energy of selected atoms in NAMD Aron Broom (Mon Sep 24 2012 - 14:06:40 CDT)
questions about accelerated MD Thomas Evangelidis (Mon Sep 24 2012 - 09:46:30 CDT)
FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Sat Sep 22 2012 - 07:41:25 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Chris Harrison (Sat Sep 22 2012 - 07:56:34 CDT)
- RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Roberts, Jason (Sat Sep 22 2012 - 20:34:50 CDT)
  - Re: RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Sun Sep 23 2012 - 11:33:31 CDT)
    - AW: RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Norman Geist (Mon Sep 24 2012 - 00:19:08 CDT)
    - Re: RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Thu Sep 27 2012 - 06:08:04 CDT)
Regarding Delta Delta G in FEP calculation snoze pa (Thu Sep 20 2012 - 13:09:57 CDT)
using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion nabaneeta mukhopadhyay (Thu Sep 20 2012 - 11:21:33 CDT)
- Re: using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion Jérôme Hénin (Thu Sep 20 2012 - 11:59:47 CDT)
  - Re: using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion nabaneeta mukhopadhyay (Thu Sep 20 2012 - 12:05:49 CDT)
    - Re: using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion Jérôme Hénin (Thu Sep 20 2012 - 12:45:49 CDT)
    - Re: using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion Aron Broom (Thu Sep 20 2012 - 12:58:35 CDT)
AMBER in NAMD Shomesankar Bhunia (Thu Sep 20 2012 - 11:12:26 CDT)
- Re: AMBER in NAMD Axel Kohlmeyer (Thu Sep 20 2012 - 11:26:05 CDT)
  - Re: AMBER in NAMD George M Giambasu (Thu Sep 20 2012 - 12:07:13 CDT)
    - Re: AMBER in NAMD Aron Broom (Thu Sep 20 2012 - 12:35:58 CDT)
zero mass particles in NAMD Markus Dahlgren (Wed Sep 19 2012 - 08:32:02 CDT)
- Re: zero mass particles in NAMD Jérôme Hénin (Wed Sep 19 2012 - 08:55:16 CDT)
AW: periodicity error Norman Geist (Tue Sep 18 2012 - 08:58:27 CDT)
periodicity error Shomesankar Bhunia (Mon Sep 17 2012 - 04:33:50 CDT)
- AW: periodicity error Norman Geist (Mon Sep 17 2012 - 09:15:29 CDT)
VMD_waterbox Shomesankar Bhunia (Mon Sep 17 2012 - 01:47:35 CDT)
- AW: VMD_waterbox Norman Geist (Mon Sep 17 2012 - 02:18:29 CDT)
AW: RE: Wrapping Norman Geist (Mon Sep 17 2012 - 01:08:36 CDT)
Re: outputting atom coordinated Ehsan Ban (Sun Sep 16 2012 - 20:01:45 CDT)
outputting atom coordinated Jacqueline Schmidt (Sun Sep 16 2012 - 16:17:25 CDT)
- AW: outputting atom coordinated Norman Geist (Mon Sep 17 2012 - 01:52:28 CDT)
n-terminus in my psfgen created pdb/psf file is missing Jacqueline Schmidt (Sun Sep 16 2012 - 11:15:41 CDT)
- Re: n-terminus in my psfgen created pdb/psf file is missing Jacqueline Schmidt (Sun Sep 16 2012 - 12:09:15 CDT)
NAMD- molecular dynamics Shomesankar Bhunia (Thu Sep 13 2012 - 14:55:14 CDT)
- Re: NAMD- molecular dynamics Aron Broom (Thu Sep 13 2012 - 17:46:17 CDT)
GTX-660 Ti benchmark Thomas Albers (Thu Sep 13 2012 - 14:50:43 CDT)
- Re: GTX-660 Ti benchmark Aron Broom (Thu Sep 13 2012 - 18:01:14 CDT)
Unable to reproduce same results in minimization with GBIS Kasam, Vinod (Thu Sep 13 2012 - 10:52:31 CDT)
- Re: Unable to reproduce same results in minimization with GBIS Chris Harrison (Thu Sep 13 2012 - 11:50:01 CDT)
  - RE: Unable to reproduce same results in minimization with GBIS Kasam, Vinod (Thu Sep 13 2012 - 13:12:24 CDT)
namd 2.9 not going so well Michael Galloway (Thu Sep 13 2012 - 10:30:09 CDT)
- AW: namd 2.9 not going so well Norman Geist (Mon Sep 17 2012 - 01:00:51 CDT)
  - Re: AW: namd 2.9 not going so well Michael Galloway (Mon Sep 17 2012 - 07:16:59 CDT)
    - AW: AW: namd 2.9 not going so well Norman Geist (Mon Sep 17 2012 - 09:23:36 CDT)
    - Re: AW: AW: namd 2.9 not going so well Michael Galloway (Tue Sep 18 2012 - 09:47:20 CDT)
problems with auto-psf gen and autoionize for ligand with atomtypes of more than 4 characters Raul Araya (Wed Sep 12 2012 - 16:34:57 CDT)
CHARMM parameters and topology for YO-PRO and/or Lucyfer Yellow Raul Araya (Wed Sep 12 2012 - 09:58:18 CDT)
ReaxFF and REBO Mikhail Suyetin (Wed Sep 12 2012 - 04:46:44 CDT)
- Re: ReaxFF and REBO Axel Kohlmeyer (Thu Sep 13 2012 - 12:02:28 CDT)
psfgen and CHARMM19 explicit exclusions Andrey (Tue Sep 11 2012 - 21:10:20 CDT)
- Re: psfgen and CHARMM19 explicit exclusions Andrey (Mon Sep 17 2012 - 22:38:24 CDT)
  - Re: Re: psfgen and CHARMM19 explicit exclusions Andrey (Thu Sep 27 2012 - 22:48:29 CDT)
    - Re: Re: psfgen and CHARMM19 explicit exclusions Chris Harrison (Fri Sep 28 2012 - 21:24:17 CDT)
    - Re: Re: psfgen and CHARMM19 explicit exclusions Andrey (Sat Sep 29 2012 - 13:04:37 CDT)
Treating Multi Chain Proteins Roy Fernando (Tue Sep 11 2012 - 14:58:14 CDT)
an error when merge pdb and psf files in vmd for big model farzad kiani (Sun Sep 09 2012 - 08:45:58 CDT)
- Re: an error when merge pdb and psf files in vmd for big model Chris Harrison (Sun Sep 09 2012 - 09:16:28 CDT)
Wrapping Buddhadev Maiti (Fri Sep 07 2012 - 22:35:10 CDT)
- RE: Wrapping Cruz-Chu Eduardo Roberto (Sat Sep 08 2012 - 14:15:05 CDT)
  - AW: RE: Wrapping Norman Geist (Mon Sep 10 2012 - 02:27:54 CDT)
namd 2.9 ibverbs issues Michael Galloway (Sat Sep 08 2012 - 12:29:12 CDT)
- AW: namd 2.9 ibverbs issues Norman Geist (Mon Sep 10 2012 - 02:22:52 CDT)
  - Re: AW: namd 2.9 ibverbs issues Michael Galloway (Mon Sep 10 2012 - 08:55:42 CDT)
    - AW: AW: namd 2.9 ibverbs issues Norman Geist (Mon Sep 10 2012 - 10:52:43 CDT)
CUDA workstation Arturas (Sat Sep 08 2012 - 11:22:49 CDT)
rmsd calculation in namd Guanglei Cui (Fri Sep 07 2012 - 14:57:59 CDT)
- Re: rmsd calculation in namd Giacomo Fiorin (Fri Sep 07 2012 - 15:36:59 CDT)
  - Re: rmsd calculation in namd Niklaus Johner (Fri Sep 07 2012 - 15:53:16 CDT)
- Re: rmsd calculation in namd Guanglei Cui (Tue Sep 11 2012 - 10:29:53 CDT)
question about "useflexiblecell' command in NAMD operation Patrick Chiu (Fri Sep 07 2012 - 14:05:32 CDT)
- Re: question about "useflexiblecell' command in NAMD operation Aron Broom (Fri Sep 07 2012 - 15:39:38 CDT)
merge pdb/psf files by psfgen - sets coordinates to zero Jacqueline Schmidt (Fri Sep 07 2012 - 13:44:49 CDT)
- Re: merge pdb/psf files by psfgen - sets coordinates to zero Chris Harrison (Fri Sep 07 2012 - 13:57:32 CDT)
[MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on" Salvatore Mario Cosseddu (Fri Sep 07 2012 - 07:49:36 CDT)
- Re: [MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on" Giacomo Fiorin (Fri Sep 07 2012 - 11:38:08 CDT)
  - Re: [MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on" Robert Elder (Sun Nov 18 2012 - 15:53:46 CST)
    - Re: [MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on" Giacomo Fiorin (Tue Nov 20 2012 - 18:41:02 CST)
namd 2.9 run instability (segfaults) Michael Galloway (Thu Sep 06 2012 - 09:19:05 CDT)
- AW: namd 2.9 run instability (segfaults) Norman Geist (Fri Sep 07 2012 - 01:10:23 CDT)
  - Re: AW: namd 2.9 run instability (segfaults) Michael Galloway (Fri Sep 07 2012 - 09:28:36 CDT)
    - AW: AW: namd 2.9 run instability (segfaults) Norman Geist (Mon Sep 10 2012 - 02:09:43 CDT)
Re: CUDA limitations Ajasja LjubetiÄ (Thu Sep 06 2012 - 08:47:40 CDT)
NAMD Run Instabilities Marc Gordon (Thu Sep 06 2012 - 08:15:58 CDT)
- Re: NAMD Run Instabilities Axel Kohlmeyer (Thu Sep 06 2012 - 08:27:08 CDT)
  - Re: NAMD Run Instabilities Marc Gordon (Mon Sep 10 2012 - 08:19:18 CDT)
- Re: NAMD Run Instabilities Ajasja LjubetiÄ (Thu Sep 06 2012 - 08:44:30 CDT)
- Re: NAMD Run Instabilities Chris Harrison (Thu Sep 06 2012 - 08:57:41 CDT)
Rückruf: scnb value to prevent VDWs scaling Norman Geist (Thu Sep 06 2012 - 08:10:22 CDT)
Reflecting boundary z axis in NAMD Ganesh Kamath (Tue Sep 04 2012 - 14:11:22 CDT)
- AW: Reflecting boundary z axis in NAMD Norman Geist (Wed Sep 05 2012 - 01:38:44 CDT)
Question of using deuterated water in NAMD Ganesh Kamath (Tue Sep 04 2012 - 13:13:27 CDT)
- Re: Question of using deuterated water in NAMD Jérôme Hénin (Tue Sep 04 2012 - 14:25:57 CDT)
restarting umbrella sampling simulation. ipsita basu (Tue Sep 04 2012 - 00:42:09 CDT)
- Re: restarting umbrella sampling simulation. Jérôme Hénin (Tue Sep 04 2012 - 02:48:15 CDT)
  - Re: restarting umbrella sampling simulation. Jérôme Hénin (Tue Sep 04 2012 - 04:31:05 CDT)
problem with pdb psf files! Jacqueline Schmidt (Sun Sep 02 2012 - 21:44:59 CDT)
- AW: problem with pdb psf files! Norman Geist (Mon Sep 03 2012 - 02:18:08 CDT)
  - Re: AW: problem with pdb psf files! Jacqueline Schmidt (Mon Sep 03 2012 - 11:01:17 CDT)
problem with pdb pdf! Jacqueline Schmidt (Sun Sep 02 2012 - 21:36:17 CDT)
Error in membrane protein simulation amin_at_imtech.res.in (Sat Sep 01 2012 - 01:59:27 CDT)
- AW: Error in membrane protein simulation Norman Geist (Mon Sep 03 2012 - 01:52:45 CDT)
  - Re: AW: Error in membrane protein simulation amin_at_imtech.res.in (Mon Sep 03 2012 - 03:41:25 CDT)
- Re: Error in membrane protein simulation JC Gumbart (Mon Sep 03 2012 - 15:51:35 CDT)
The size of a periodic cell in NAMD operation Patrick Chiu (Fri Aug 31 2012 - 18:45:19 CDT)
- Re: The size of a periodic cell in NAMD operation Chris Harrison (Fri Aug 31 2012 - 19:55:42 CDT)
  - AW: The size of a periodic cell in NAMD operation Norman Geist (Mon Sep 03 2012 - 01:45:48 CDT)
NAMD 2.9 with CUDA runs Ashley Chew (Fri Aug 31 2012 - 04:02:48 CDT)
- Re: NAMD 2.9 with CUDA runs Chris Harrison (Fri Aug 31 2012 - 13:14:02 CDT)
  - Re: NAMD 2.9 with CUDA runs Peter Jones (Fri Aug 31 2012 - 21:41:25 CDT)
    - Re: NAMD 2.9 with CUDA runs Chris Harrison (Sat Sep 01 2012 - 20:02:28 CDT)
    - AW: NAMD 2.9 with CUDA runs Norman Geist (Mon Sep 03 2012 - 01:30:46 CDT)
  - RE: NAMD 2.9 with CUDA runs Ashley Chew (Sun Sep 02 2012 - 20:37:30 CDT)
Oscillating Electric Field Quick, Ross (Fri Aug 31 2012 - 11:26:39 CDT)
- Re: Oscillating Electric Field Cruz-Chu Eduardo Roberto (Fri Aug 31 2012 - 11:45:42 CDT)
Re: dump specific atom positions into a txt file during the simulation Jacqueline Schmidt (Fri Aug 31 2012 - 03:15:56 CDT)
- Re: dump specific atom positions into a txt file during the simulation Ajasja LjubetiÄ (Fri Aug 31 2012 - 03:44:42 CDT)
  - Re: dump specific atom positions into a txt file during the simulation Jacqueline Schmidt (Fri Aug 31 2012 - 07:33:40 CDT)
dump specific atom positions into a txt file during the simulation Jacqueline Schmidt (Fri Aug 31 2012 - 01:14:09 CDT)
AW: AW: simulation:protein,ligand,lipid,water and ions Norman Geist (Fri Aug 31 2012 - 00:47:21 CDT)
NAMD on Peta-Scale Machines Yim, Keun Soo (Thu Aug 30 2012 - 13:19:10 CDT)
- NAMD on Peta-Scale Machines Yim, Keun Soo (Fri Aug 31 2012 - 18:08:13 CDT)
  - Re: NAMD on Peta-Scale Machines Wang Yi (Sat Sep 01 2012 - 12:18:12 CDT)
  - Re: NAMD on Peta-Scale Machines Axel Kohlmeyer (Sun Sep 02 2012 - 07:19:02 CDT)
    - Re: NAMD on Peta-Scale Machines Iyer, Ravishankar K (Sun Sep 02 2012 - 11:07:32 CDT)
NBTABLE issue Arturas (Thu Aug 30 2012 - 13:45:14 CDT)
AW: simulation:protein,ligand,lipid,water and ions Norman Geist (Thu Aug 30 2012 - 09:47:47 CDT)
NAMD 2.8 and PLUMED 1.3 candy deck (Thu Aug 30 2012 - 07:59:41 CDT)
- Re: NAMD 2.8 and PLUMED 1.3 Aron Broom (Fri Aug 31 2012 - 13:57:31 CDT)
  - AW: NAMD 2.8 and PLUMED 1.3 Norman Geist (Mon Sep 03 2012 - 01:34:07 CDT)
  - RE: NAMD 2.8 and PLUMED 1.3 Buddhadev Maiti (Fri Aug 31 2012 - 22:40:11 CDT)
Re: Re: Chris Harrison (Thu Aug 30 2012 - 03:25:09 CDT)
AW: question regarding simulated annealing Norman Geist (Thu Aug 30 2012 - 02:56:04 CDT)
question and NAMD operation Patrick Chiu (Wed Aug 29 2012 - 15:19:36 CDT)
- Re: question and NAMD operation snoze pa (Wed Aug 29 2012 - 15:33:48 CDT)
  - AW: question and NAMD operation Norman Geist (Thu Aug 30 2012 - 02:16:40 CDT)
- Re: question and NAMD operation Chris Harrison (Wed Aug 29 2012 - 15:45:39 CDT)
Accelerated MD Thomas Albers (Wed Aug 29 2012 - 15:06:04 CDT)
- Re: Accelerated MD Chris Harrison (Wed Aug 29 2012 - 15:37:06 CDT)
  - Re: Accelerated MD Thomas Albers (Wed Aug 29 2012 - 15:53:43 CDT)
  - Re: Accelerated MD Thomas Albers (Wed Aug 29 2012 - 21:38:20 CDT)
- Re: Accelerated MD Jeff Wereszczynski (Wed Aug 29 2012 - 15:47:31 CDT)
  - Re: Accelerated MD Thomas Albers (Wed Aug 29 2012 - 16:20:50 CDT)
Question regarding FEP parameters snoze pa (Wed Aug 29 2012 - 13:05:15 CDT)
- Re: Question regarding FEP parameters snoze pa (Wed Aug 29 2012 - 13:47:31 CDT)
  - Re: Question regarding FEP parameters Chris Harrison (Wed Aug 29 2012 - 15:32:52 CDT)
    - Re: vmd-l: Re: Question regarding FEP parameters snoze pa (Fri Aug 31 2012 - 12:06:48 CDT)
    - Re: vmd-l: Re: Question regarding FEP parameters Chris Harrison (Fri Aug 31 2012 - 20:06:54 CDT)
(no subject) Jacqueline Schmidt (Wed Aug 29 2012 - 11:06:10 CDT)
- (no subject) Suranga Edirisinghe (Wed Aug 29 2012 - 16:13:55 CDT)
  - AW: Re: Norman Geist (Thu Aug 30 2012 - 02:32:29 CDT)
Run NAMD binaries Monika Madhavi (Wed Aug 29 2012 - 03:58:12 CDT)
- Re: Run NAMD binaries Axel Kohlmeyer (Wed Aug 29 2012 - 04:30:20 CDT)
  - Re: Run NAMD binaries Suranga Edirisinghe (Wed Aug 29 2012 - 09:26:39 CDT)
Warning: Not all atoms have unique coordinates Jacqueline Schmidt (Tue Aug 28 2012 - 19:17:54 CDT)
- AW: Warning: Not all atoms have unique coordinates Norman Geist (Thu Aug 30 2012 - 01:54:20 CDT)
namd simulationâ€‹:protein,lâ€‹igand,lipiâ€‹d,water and ions Marlet Martinez (Tue Aug 28 2012 - 12:30:04 CDT)
- AW: namd simulationâ€‹:protein,lâ€‹igand,lipiâ€‹d,water and ions Norman Geist (Thu Aug 30 2012 - 02:06:14 CDT)
Namd list: "Size cell" for restart Mariana Graterol (Tue Aug 28 2012 - 08:07:03 CDT)
- Re: Namd list: "Size cell" for restart Axel Kohlmeyer (Tue Aug 28 2012 - 11:01:51 CDT)
  - Re: Namd list: "Size cell" for restart Suranga Edirisinghe (Tue Aug 28 2012 - 13:45:03 CDT)
    - AW: Namd list: "Size cell" for restart Norman Geist (Thu Aug 30 2012 - 01:59:07 CDT)
simulation of non-rectangular surface Jacqueline Schmidt (Tue Aug 28 2012 - 10:20:02 CDT)
- Re: simulation of non-rectangular surface Axel Kohlmeyer (Tue Aug 28 2012 - 10:39:07 CDT)
  - Re: simulation of non-rectangular surface Jacqueline Schmidt (Tue Aug 28 2012 - 15:34:50 CDT)
question regarding simulated annealing Puspita Halder (Tue Aug 28 2012 - 07:03:39 CDT)
- AW: question regarding simulated annealing Norman Geist (Thu Aug 30 2012 - 01:50:11 CDT)
- Re: question regarding simulated annealing Chris Harrison (Thu Aug 30 2012 - 02:28:00 CDT)
  - Re: question regarding simulated annealing Puspita Halder (Thu Aug 30 2012 - 08:15:51 CDT)
    - Re: question regarding simulated annealing Puspita Halder (Fri Aug 31 2012 - 00:46:05 CDT)
    - Re: question regarding simulated annealing Chris Harrison (Mon Sep 10 2012 - 23:17:47 CDT)
water parameters Mark Abraham (Mon Aug 27 2012 - 18:29:25 CDT)
need help in using colvars option sudipta (Mon Aug 27 2012 - 17:41:51 CDT)
- Re: need help in using colvars option Giacomo Fiorin (Mon Aug 27 2012 - 17:54:09 CDT)
  - Re: need help in using colvars option Aron Broom (Tue Aug 28 2012 - 12:17:20 CDT)
NAMD pulling one domain snoze pa (Mon Aug 27 2012 - 14:36:34 CDT)
- Re: NAMD pulling one domain Wang Yi (Mon Aug 27 2012 - 14:40:22 CDT)
  - Re: NAMD pulling one domain snoze pa (Wed Aug 29 2012 - 09:58:49 CDT)
    - Re: NAMD pulling one domain Wang Yi (Wed Aug 29 2012 - 10:05:44 CDT)
The structure files for the second turn of simulation yp sun (Sun Aug 26 2012 - 20:30:04 CDT)
- AW: The structure files for the second turn of simulation Norman Geist (Tue Aug 28 2012 - 02:10:17 CDT)
Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0 Mariana Graterol (Sun Aug 26 2012 - 14:07:17 CDT)
- Re: Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0 Suranga Edirisinghe (Mon Aug 27 2012 - 12:28:30 CDT)
  - Re: Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0 subbarao kanchi (Mon Aug 27 2012 - 13:59:03 CDT)
    - AW: Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0 Norman Geist (Tue Aug 28 2012 - 02:00:12 CDT)
Water bubbles in NVT equilibration dynamics Mariana Graterol (Fri Aug 24 2012 - 18:52:28 CDT)
- Re: Water bubbles in NVT equilibration dynamics Ana Celia Vila Verde (Mon Aug 27 2012 - 09:23:51 CDT)
  - Re: Water bubbles in NVT equilibration dynamics Jeffrey Potoff (Mon Aug 27 2012 - 10:00:39 CDT)
    - AW: Water bubbles in NVT equilibration dynamics Norman Geist (Tue Aug 28 2012 - 01:26:25 CDT)
Functional form to apply constraints Mariana Graterol (Fri Aug 24 2012 - 18:28:43 CDT)
what is fullSamples? ¼¿ëÀÏ (Sun Aug 26 2012 - 22:56:59 CDT)
- Re: what is fullSamples? Jérôme Hénin (Tue Aug 28 2012 - 06:25:52 CDT)
(no subject) ¼¿ëÀÏ (Sun Aug 26 2012 - 22:55:40 CDT)
restraining Christopher Rowley (Thu Aug 23 2012 - 13:55:59 CDT)
- Re: restraining Chris Harrison (Thu Aug 23 2012 - 22:08:49 CDT)
  - Re: restraining Christopher Rowley (Thu Aug 23 2012 - 22:20:55 CDT)
  - Re: restraining Axel Kohlmeyer (Fri Aug 24 2012 - 03:09:54 CDT)
equilibrate glycerol molecules Namd Namd (Thu Aug 23 2012 - 03:45:32 CDT)
- Re: equilibrate glycerol molecules Axel Kohlmeyer (Thu Aug 23 2012 - 04:04:34 CDT)
shift the molecules oguz gurbulak (Thu Aug 23 2012 - 03:29:53 CDT)
- Re: shift the molecules Chris Harrison (Thu Aug 23 2012 - 22:38:51 CDT)
Sr2+ Maria Bykhovskaia (Wed Aug 22 2012 - 14:54:38 CDT)
has system reached a steady state condition? farzad kiani (Wed Aug 22 2012 - 06:11:06 CDT)
- Fw: has system reached a steady state condition? farzad kiani (Wed Aug 22 2012 - 06:14:25 CDT)
NPT at 100 bar Francesco Pietra (Wed Aug 22 2012 - 03:02:03 CDT)
- Re: NPT at 100 bar Jernej Zidar (Wed Aug 22 2012 - 03:05:52 CDT)
  - Re: NPT at 100 bar Francesco Pietra (Wed Aug 22 2012 - 04:37:57 CDT)
    - Re: NPT at 100 bar Axel Kohlmeyer (Wed Aug 22 2012 - 04:53:31 CDT)
umbrella sampling ipsita basu (Wed Aug 22 2012 - 01:52:14 CDT)
- Re: umbrella sampling Jérôme Hénin (Wed Aug 22 2012 - 03:10:17 CDT)
AW: GPU workstation build Norman Geist (Tue Aug 21 2012 - 09:33:48 CDT)
No output after "scheduler running in netpoll mode" amin_at_imtech.res.in (Tue Aug 21 2012 - 08:58:40 CDT)
- AW: No output after "scheduler running in netpoll mode" Norman Geist (Tue Aug 21 2012 - 09:39:35 CDT)
  - Re: AW: No output after "scheduler running in netpoll mode" amin_at_imtech.res.in (Tue Aug 21 2012 - 11:43:20 CDT)
    - AW: AW: No output after "scheduler running in netpoll mode" Norman Geist (Wed Aug 22 2012 - 01:35:50 CDT)
Fwd: GPU workstation build Francesco Pietra (Tue Aug 21 2012 - 08:44:09 CDT)
Displaying the gradient tolerance in the output Webber (Tue Aug 21 2012 - 03:46:25 CDT)
- Re: Displaying the gradient tolerance in the output Chris Harrison (Thu Aug 23 2012 - 22:52:31 CDT)
energy minimization yandong Huang (Mon Aug 20 2012 - 23:24:30 CDT)
- Re: energy minimization Aaron Oakley (Mon Aug 20 2012 - 23:45:51 CDT)
  - Re: energy minimization Aron Broom (Tue Aug 21 2012 - 00:47:47 CDT)
  - AW: energy minimization Norman Geist (Tue Aug 21 2012 - 01:24:22 CDT)
GPU workstation build Blake Mertz (Mon Aug 20 2012 - 10:41:13 CDT)
- Re: GPU workstation build Aron Broom (Mon Aug 20 2012 - 11:21:10 CDT)
  - AW: GPU workstation build Norman Geist (Tue Aug 21 2012 - 01:22:49 CDT)
- unsubscribe Yuqi Liu (Mon Aug 20 2012 - 18:23:00 CDT)
Displaying the gradient tolerance in the output as the example output from tutorial 1-2 Water Sphere Webber (Sun Aug 19 2012 - 19:02:29 CDT)
- Re: Displaying the gradient tolerance in the output as the example output from tutorial 1-2 Water Sphere Webber (Tue Aug 21 2012 - 01:57:53 CDT)
Calculating Potential Energy for an atom selection Aron Broom (Fri Aug 17 2012 - 15:49:38 CDT)
- Re: Calculating Potential Energy for an atom selection Axel Kohlmeyer (Fri Aug 17 2012 - 15:57:41 CDT)
  - Re: Calculating Potential Energy for an atom selection Aron Broom (Sun Aug 19 2012 - 20:03:19 CDT)
multiple dynamic sections in the config file? Jacqueline Schmidt (Thu Aug 16 2012 - 19:03:44 CDT)
- Re: multiple dynamic sections in the config file? Chris Harrison (Thu Aug 23 2012 - 22:55:50 CDT)
shift the molecules oguz gurbulak (Thu Aug 16 2012 - 03:13:10 CDT)
- Re: shift the molecules Axel Kohlmeyer (Thu Aug 16 2012 - 03:56:25 CDT)
equilibrate conf file Namd Namd (Thu Aug 16 2012 - 02:56:30 CDT)
- Re: equilibrate conf file Axel Kohlmeyer (Thu Aug 16 2012 - 03:54:48 CDT)
Evaluate Work for Targeted Molecular Dynamics Simulations Mert Gür (Wed Aug 15 2012 - 16:08:52 CDT)
Multiple gpu cards Dr. Eddie (Wed Aug 15 2012 - 09:24:46 CDT)
- Re: Multiple gpu cards Axel Kohlmeyer (Wed Aug 15 2012 - 09:54:10 CDT)
- AW: Multiple gpu cards Norman Geist (Wed Aug 15 2012 - 09:58:14 CDT)
inputPrefix in ABF Branko (Tue Aug 14 2012 - 12:04:57 CDT)
- Re: inputPrefix in ABF Jérôme Hénin (Thu Aug 16 2012 - 01:51:44 CDT)
  - Re: inputPrefix in ABF Branko (Thu Aug 16 2012 - 04:02:32 CDT)
pressure profile calculations JC Gumbart (Mon Aug 13 2012 - 21:11:20 CDT)
- Re: pressure profile calculations Grace Brannigan (Thu Aug 16 2012 - 14:33:21 CDT)
  - Re: pressure profile calculations Grace Brannigan (Fri Aug 17 2012 - 06:16:21 CDT)
  - Re: pressure profile calculations JC Gumbart (Sat Aug 18 2012 - 18:24:08 CDT)
    - Re: pressure profile calculations Grace Brannigan (Mon Aug 20 2012 - 11:22:12 CDT)
    - Re: pressure profile calculations JC Gumbart (Mon Aug 20 2012 - 20:58:53 CDT)
scnb value to prevent VDWs scaling Marc Gordon (Mon Aug 13 2012 - 08:40:13 CDT)
- Re: scnb value to prevent VDWs scaling Marc Gordon (Thu Sep 06 2012 - 07:26:55 CDT)
  - AW: scnb value to prevent VDWs scaling Norman Geist (Thu Sep 06 2012 - 08:09:22 CDT)
  - Re: scnb value to prevent VDWs scaling Marc Gordon (Sat Sep 08 2012 - 05:21:49 CDT)
1-4 vdw scaling? Jacqueline Schmidt (Sat Aug 11 2012 - 14:41:20 CDT)
- Re: 1-4 vdw scaling? Axel Kohlmeyer (Sat Aug 11 2012 - 14:49:03 CDT)
Namd, lammps comparing energies Jacqueline Schmidt (Fri Aug 10 2012 - 12:44:05 CDT)
- Re: Namd, lammps comparing energies Giacomo Fiorin (Fri Aug 10 2012 - 13:20:21 CDT)
- Re: Namd, lammps comparing energies Axel Kohlmeyer (Fri Aug 10 2012 - 15:56:18 CDT)
RE: openAtom/NAMD2.9 implementation Bennion, Brian (Thu Aug 09 2012 - 12:17:57 CDT)
residue_rmsd.tcl via Branko (Thu Aug 09 2012 - 07:50:56 CDT)
- RE: residue_rmsd.tcl via Michel Espinoza-Fonseca (Thu Aug 09 2012 - 08:18:40 CDT)
  - Re: residue_rmsd.tcl via Branko (Thu Aug 09 2012 - 08:38:14 CDT)
    - AW: residue_rmsd.tcl via Norman Geist (Thu Aug 09 2012 - 09:44:28 CDT)
win64 namd cuda: compile? Aaron Cann (Tue Aug 07 2012 - 00:09:36 CDT)
- Re: win64 namd cuda: compile? Axel Kohlmeyer (Tue Aug 07 2012 - 03:46:35 CDT)
fep/parm7 Francesco Pietra (Mon Aug 06 2012 - 10:57:36 CDT)
Newbie's question Theresa H (Mon Aug 06 2012 - 09:46:49 CDT)
- Newbie's question Theresa H (Mon Aug 06 2012 - 12:41:18 CDT)
  - AW: Newbie's question Norman Geist (Tue Aug 07 2012 - 00:25:25 CDT)
  - Re: Newbie's question Axel Kohlmeyer (Tue Aug 07 2012 - 03:38:50 CDT)
Alchemical protein transformation with a group of (non proteic) atoms bound to two amino acids Francesco Pietra (Mon Aug 06 2012 - 02:36:47 CDT)
connect a spring between all the atoms present in pdb structure SONY kaur (Sat Aug 04 2012 - 04:31:42 CDT)
- Re: vmd-l: connect a spring between all the atoms present in pdb structure Axel Kohlmeyer (Sat Aug 04 2012 - 13:20:05 CDT)
- Re: connect a spring between all the atoms present in pdb structure Axel Kohlmeyer (Sat Aug 04 2012 - 13:21:27 CDT)
- Re: vmd-l: connect a spring between all the atoms present in pdb structure Eduard Schreiner (Sat Aug 04 2012 - 16:36:38 CDT)
Re: How to create psf for graphene Monika Madhavi (Sat Aug 04 2012 - 01:04:24 CDT)
- Re: How to create psf for graphene Axel Kohlmeyer (Sat Aug 04 2012 - 13:28:04 CDT)
How to create psf for graphene Monika Madhavi (Fri Aug 03 2012 - 22:35:28 CDT)
accelerated MD (aMD) with GPU Jiyong Park (Fri Aug 03 2012 - 17:48:42 CDT)
how do I pass environmental variables to namd on BlueGene/P? Aaron Oakley (Thu Aug 02 2012 - 23:39:06 CDT)
no output for corrfunc Rui Zhang (Thu Aug 02 2012 - 19:06:25 CDT)
- Re: no output for corrfunc Giacomo Fiorin (Thu Aug 02 2012 - 19:15:51 CDT)
  - Re: no output for corrfunc Rui Zhang (Fri Aug 03 2012 - 10:30:49 CDT)
- Re: no output for corrfunc Giacomo Fiorin (Mon Aug 06 2012 - 11:20:37 CDT)
  - Re: no output for corrfunc Rui Zhang (Tue Aug 07 2012 - 18:11:32 CDT)
  - Re: no output for corrfunc Robert Elder (Thu Nov 01 2012 - 18:26:23 CDT)
RMSD difference on alignment of two states of protein in VMD and NAMD TMD Nikita chopra (Thu Aug 02 2012 - 15:27:36 CDT)
Drude polarizable models with namd Ana Celia Vila Verde (Thu Aug 02 2012 - 11:11:08 CDT)
LCPO SASA Calculation on the GPU Aron Broom (Wed Aug 01 2012 - 22:44:09 CDT)
restarting ABF Branko (Wed Aug 01 2012 - 10:13:29 CDT)
- Re: restarting ABF Giacomo Fiorin (Wed Aug 01 2012 - 10:23:30 CDT)
  - Re: restarting ABF Giacomo Fiorin (Wed Aug 01 2012 - 10:53:56 CDT)
  - Re: restarting ABF Jérôme Hénin (Wed Aug 01 2012 - 11:20:23 CDT)
laptop GPU support Thomas Evangelidis (Wed Aug 01 2012 - 05:27:58 CDT)
- Re: laptop GPU support Axel Kohlmeyer (Wed Aug 01 2012 - 06:23:32 CDT)
Re: peculiar scaling on the GPU Axel Kohlmeyer (Wed Aug 01 2012 - 01:40:56 CDT)
(no subject) Sean T Kigerl (Tue Jul 31 2012 - 18:27:12 CDT)
- Re: Aron Broom (Tue Jul 31 2012 - 19:35:32 CDT)
NAMD 2.9: Segmentation fault? María Antonieta Sánchez Farrán (Tue Jul 31 2012 - 12:44:09 CDT)
- Re: NAMD 2.9: Segmentation fault? Aron Broom (Tue Jul 31 2012 - 12:52:37 CDT)
peculiar scaling on the GPU Ajasja LjubetiÄ (Tue Jul 31 2012 - 09:06:50 CDT)
- AW: peculiar scaling on the GPU Norman Geist (Wed Aug 01 2012 - 01:14:26 CDT)
Uneven sampling when using ABF DAI, JIAN (Mon Jul 30 2012 - 12:38:12 CDT)
- Re: Uneven sampling when using ABF Aron Broom (Mon Jul 30 2012 - 18:10:03 CDT)
  - Re: Uneven sampling when using ABF JC Gumbart (Mon Jul 30 2012 - 20:15:02 CDT)
openAtom/NAMD2.9 implementation Bennion, Brian (Mon Jul 30 2012 - 11:59:29 CDT)
Uneven sampling in using ABF DAI, JIAN (Mon Jul 30 2012 - 08:17:45 CDT)
Low CPU usage with NAMD running on linux cluster amin_at_imtech.res.in (Sat Jul 28 2012 - 01:33:17 CDT)
- Re: Low CPU usage with NAMD running on linux cluster Branko (Sat Jul 28 2012 - 07:52:17 CDT)
AW: Atoms moving too fast with NAMD/Amber Norman Geist (Fri Jul 27 2012 - 03:39:33 CDT)
Random seed and equilibrated structure Dr. Eddie (Thu Jul 26 2012 - 15:55:13 CDT)
- Re: Random seed and equilibrated structure Aron Broom (Thu Jul 26 2012 - 16:07:32 CDT)
  - Re: Random seed and equilibrated structure Dr. Eddie (Thu Jul 26 2012 - 16:40:05 CDT)
    - AW: Random seed and equilibrated structure Norman Geist (Fri Jul 27 2012 - 01:50:17 CDT)
    - Re: Random seed and equilibrated structure Axel Kohlmeyer (Fri Jul 27 2012 - 03:52:15 CDT)
startup phase 8: not complete! mj_aghaei_at_aut.ac.ir (Wed Jul 25 2012 - 21:12:31 CDT)
namd crashes after 300K steps Peter Jones (Thu Jul 26 2012 - 03:06:17 CDT)
Atoms moving too fast with NAMD/Amber Francesco Pietra (Thu Jul 26 2012 - 00:48:46 CDT)
- AW: Atoms moving too fast with NAMD/Amber Norman Geist (Thu Jul 26 2012 - 01:42:42 CDT)
problem with NAMD surface area calculation (LCPO) -- fixed Clayton (Mon Jul 23 2012 - 10:08:35 CDT)
drude water in namd Sandeep Patel (Tue Jul 24 2012 - 16:07:50 CDT)
- Re: drude water in namd David Hardy (Tue Jul 24 2012 - 16:22:57 CDT)
secondary structure restraints in coarse grain Eun Kim (Tue Jul 24 2012 - 13:35:00 CDT)
- Re: secondary structure restraints in coarse grain Aron Broom (Tue Jul 24 2012 - 15:37:54 CDT)
  - Re: secondary structure restraints in coarse grain Jesper Sørensen (Tue Jul 24 2012 - 16:35:37 CDT)
CNT builder farzad kiani (Tue Jul 24 2012 - 09:25:23 CDT)
Error: periodicity of dihedral zero Francesco Pietra (Tue Jul 24 2012 - 03:23:19 CDT)
Tabulated potential Adam Skelton (Mon Jul 23 2012 - 16:17:35 CDT)
- Re: Tabulated potential Adam Skelton (Thu Jul 26 2012 - 13:30:54 CDT)
Lenard Jones coefficients for Neon atoms Roy Fernando (Mon Jul 23 2012 - 08:53:39 CDT)
Keeping water out of the binding pocket with ColVar Wang Yi (Fri Jul 20 2012 - 20:14:41 CDT)
- Re: Keeping water out of the binding pocket with ColVar Aron Broom (Fri Jul 20 2012 - 20:19:09 CDT)
  - Re: Keeping water out of the binding pocket with ColVar Wang Yi (Fri Jul 20 2012 - 20:21:30 CDT)
    - Re: Keeping water out of the binding pocket with ColVar JC Gumbart (Fri Jul 20 2012 - 23:44:19 CDT)
crossterm error Cristhian Boetsch (Fri Jul 20 2012 - 13:06:04 CDT)
- Re: crossterm error Dr. Eddie (Thu Jul 26 2012 - 15:56:46 CDT)
constant velocity of carbon nanotube through water bond.james (Fri Jul 20 2012 - 00:11:27 CDT)
- Re: constant velocity of carbon nanotube through water Axel Kohlmeyer (Fri Jul 20 2012 - 01:42:11 CDT)
- Re: constant velocity of carbon nanotube through water Cruz-Chu Eduardo Roberto (Fri Jul 20 2012 - 03:25:11 CDT)
  - Re:Re: constant velocity of carbon nanotube through water bond.james (Fri Jul 20 2012 - 05:41:56 CDT)
    - Re: constant velocity of carbon nanotube through water Cruz-Chu Eduardo Roberto (Fri Jul 20 2012 - 05:46:13 CDT)
different seeds and protein behavior Dr. Eddie (Thu Jul 19 2012 - 18:29:21 CDT)
- Re: different seeds and protein behavior Aron Broom (Thu Jul 19 2012 - 20:21:44 CDT)
  - Re: different seeds and protein behavior Nicholas M Glykos (Fri Jul 20 2012 - 03:14:17 CDT)
- Re: different seeds and protein behavior amin_at_imtech.res.in (Thu Jul 19 2012 - 21:36:23 CDT)
NAMD2.9 Release and Multi-GPU Minimization Errors c jepson (Thu Jul 19 2012 - 15:15:32 CDT)
no CUDA-capable device is detected Damián Montaldo (Thu Jul 19 2012 - 14:12:06 CDT)
Generalized Born Solvent Question Aron Broom (Thu Jul 19 2012 - 13:34:34 CDT)
- Re: Generalized Born Solvent Question Aron Broom (Mon Jul 30 2012 - 17:06:54 CDT)
  - Re: Generalized Born Solvent Question Roy Fernando (Fri Aug 03 2012 - 14:07:26 CDT)
NAMD does not exit simulation on satisfying condition in the tclforces script Mithun Biswas (Thu Jul 19 2012 - 10:26:01 CDT)
- Re: NAMD does not exit simulation on satisfying condition in the tclforces script Mithun Biswas (Thu Jul 26 2012 - 08:21:23 CDT)
Running Parallel Jobs Simultaneously with MPIRUN Rajan Vatassery (Wed Jul 18 2012 - 10:36:04 CDT)
- Re: Running Parallel Jobs Simultaneously with MPIRUN Axel Kohlmeyer (Wed Jul 18 2012 - 11:33:46 CDT)
  - Re: Running Parallel Jobs Simultaneously with MPIRUN Rajan Vatassery (Wed Jul 18 2012 - 14:28:07 CDT)
Instabilities in Minimization Sándor Kovács (Tue Jul 17 2012 - 17:14:10 CDT)
- Re: Instabilities in Minimization Aron Broom (Tue Jul 17 2012 - 17:34:38 CDT)
  - Re: Instabilities in Minimization JC Gumbart (Tue Jul 17 2012 - 17:50:58 CDT)
Cuda error Dr. Eddie (Mon Jul 16 2012 - 13:19:19 CDT)
- Re: Cuda error Aron Broom (Mon Jul 16 2012 - 13:30:57 CDT)
  - Aspirin charmm ff Ramin Ekhteiari (Tue Jul 17 2012 - 10:21:13 CDT)
(no subject) ÖÓË´ (Mon Jul 16 2012 - 08:59:14 CDT)
- AW: Norman Geist (Tue Jul 17 2012 - 00:35:19 CDT)
postdoctoral position available in simulations of ionic liquids at NASA Ames Lawson, John W. (ARC-TSM) (Mon Jul 16 2012 - 00:35:46 CDT)
Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Roy Fernando (Sun Jul 15 2012 - 17:13:22 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Aron Broom (Sun Jul 15 2012 - 20:31:26 CDT)
  - Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Ajasja LjubetiÄ (Mon Jul 16 2012 - 01:25:10 CDT)
  - Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Roy Fernando (Mon Jul 16 2012 - 15:03:53 CDT)
gentoo ebuild Dr. Eddie (Fri Jul 13 2012 - 16:01:12 CDT)
- Re: gentoo ebuild Aron Broom (Fri Jul 13 2012 - 16:03:23 CDT)
Am I doing the Right Thing? Roy Fernando (Thu Jul 12 2012 - 12:02:05 CDT)
- Re: Am I doing the Right Thing? Aron Broom (Thu Jul 12 2012 - 12:10:43 CDT)
  - Re: Am I doing the Right Thing? Roy Fernando (Thu Jul 12 2012 - 12:31:36 CDT)
gtx-680: CUDA error in cudaGetDeviceCount lcbllcc_at_gmail.com (Thu Jul 12 2012 - 04:28:08 CDT)
Re: vmd-l: vmd installation problem oguz gurbulak (Thu Jul 12 2012 - 00:59:23 CDT)
How does NAMD treat a bond across periodic boundaries mj_aghaei_at_aut.ac.ir (Wed Jul 11 2012 - 23:17:49 CDT)
- Re: How does NAMD treat a bond across periodic boundaries Axel Kohlmeyer (Thu Jul 12 2012 - 01:56:00 CDT)
umbrella sampling ipsita basu (Wed Jul 11 2012 - 06:48:16 CDT)
- Re: umbrella sampling Jérôme Hénin (Wed Jul 11 2012 - 10:20:58 CDT)
  - Re: umbrella sampling ipsita basu (Thu Jul 12 2012 - 01:17:53 CDT)
    - Re: umbrella sampling Aron Broom (Thu Jul 12 2012 - 07:46:50 CDT)
Alchemical with parm7 ff Francesco Pietra (Wed Jul 11 2012 - 03:39:30 CDT)
What is a good (small) test system for NAMD Roy Fernando (Tue Jul 10 2012 - 14:13:01 CDT)
- Re: What is a good (small) test system for NAMD Giacomo Fiorin (Tue Jul 10 2012 - 14:17:41 CDT)
Running NAMD on Forge (CUDA) Gianluca Interlandi (Tue Jul 10 2012 - 12:14:52 CDT)
- Re: Running NAMD on Forge (CUDA) Aron Broom (Tue Jul 10 2012 - 12:21:45 CDT)
  - Re: Running NAMD on Forge (CUDA) Gianluca Interlandi (Thu Jul 12 2012 - 13:41:16 CDT)
force field parameters for Silicon farzad kiani (Tue Jul 10 2012 - 07:57:05 CDT)
Re: Fixing bonds in dihydrogen phosphate to save computation time Axel Kohlmeyer (Tue Jul 10 2012 - 05:21:14 CDT)
- AW: Fixing bonds in dihydrogen phosphate to save computation time Norman Geist (Tue Jul 10 2012 - 05:36:15 CDT)
Re: Multi core problem Axel Kohlmeyer (Tue Jul 10 2012 - 05:18:28 CDT)
pairlist violations Thomas Brian (Mon Jul 09 2012 - 18:44:55 CDT)
- Re: pairlist violations francesco oteri (Tue Jul 10 2012 - 03:40:42 CDT)
- Re: pairlist violations Axel Kohlmeyer (Tue Jul 10 2012 - 05:24:01 CDT)
  - Re: pairlist violations JC Gumbart (Tue Jul 10 2012 - 12:25:08 CDT)
    - Re: pairlist violations Thomas Brian (Tue Jul 10 2012 - 15:15:07 CDT)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 22-26, 2012 in Urbana, Illinois David Brandon (Mon Jul 09 2012 - 14:29:08 CDT)
Fixing bonds in dihydrogen phosphate to save computation time Evgeny Bulat (Mon Jul 09 2012 - 13:55:45 CDT)
- AW: Fixing bonds in dihydrogen phosphate to save computation time Norman Geist (Tue Jul 10 2012 - 00:44:57 CDT)
Multi core problem flavio seixas (Sun Jul 08 2012 - 14:48:04 CDT)
- AW: Multi core problem Norman Geist (Tue Jul 10 2012 - 00:38:51 CDT)
periodic boundaries farzad kiani (Sat Jul 07 2012 - 05:51:22 CDT)
- AW: periodic boundaries Norman Geist (Tue Jul 10 2012 - 00:30:50 CDT)
steered molecular dynamics with multiple molecules Koivuniemi Artturi (Wed Jul 04 2012 - 05:19:15 CDT)
- Re: steered molecular dynamics with multiple molecules Jérôme Hénin (Thu Jul 05 2012 - 05:10:50 CDT)
testing digest demime - please ignore #2 Jim Phillips (Tue Jul 03 2012 - 19:59:09 CDT)
testing digest demime - please ignore Jim Phillips (Tue Jul 03 2012 - 17:50:18 CDT)
Compiling and running NAMD on multiple nodes of SDSC Trestles Gianluca Interlandi (Tue Jul 03 2012 - 13:28:36 CDT)
- Re: Compiling and running NAMD on multiple nodes of SDSC Trestles Gianluca Interlandi (Tue Jul 03 2012 - 16:22:21 CDT)
one-sided harmonic restraint potential Sandeep Patel (Mon Jul 02 2012 - 21:51:21 CDT)
- Re: one-sided harmonic restraint potential Giacomo Fiorin (Mon Jul 02 2012 - 21:59:42 CDT)
about dcd files Namd Namd (Mon Jul 02 2012 - 08:30:17 CDT)
- Re: about dcd files Axel Kohlmeyer (Mon Jul 02 2012 - 09:00:43 CDT)
Targeted Molecular Dynamics Thomas Albers (Sat Jun 30 2012 - 14:56:53 CDT)
- Re: Targeted Molecular Dynamics Aron Broom (Sat Jun 30 2012 - 17:13:59 CDT)
pbc precision Thomas Brian (Thu Jun 28 2012 - 15:18:10 CDT)
Re: efield energies incorrect in analysis mode (run 0) ? Mark Triger (Thu Jun 28 2012 - 14:22:18 CDT)
namd cuda error. kanchi subbarao rao (Thu Jun 28 2012 - 11:13:43 CDT)
- Fwd: namd cuda error. kanchi subbarao rao (Tue Jul 03 2012 - 00:20:01 CDT)
  - Re: namd cuda error. kanchi subbarao rao (Tue Jul 03 2012 - 10:03:59 CDT)
wrap dcd files Namd Namd (Thu Jun 28 2012 - 05:03:10 CDT)
- AW: wrap dcd files Norman Geist (Thu Jun 28 2012 - 06:10:17 CDT)
  - AW: wrap dcd files Namd Namd (Thu Jun 28 2012 - 07:25:22 CDT)
RE: namd-l digest V1 #787 Hyuntae Na (Wed Jun 27 2012 - 20:22:15 CDT)
efield energies incorrect in analysis mode (run 0) ? Mark Triger (Wed Jun 27 2012 - 16:25:04 CDT)
- AW: efield energies incorrect in analysis mode (run 0) ? Norman Geist (Thu Jun 28 2012 - 00:29:32 CDT)
efield energies incorrect in analysis mode (run 0) ? Mark Triger (Wed Jun 27 2012 - 13:19:48 CDT)
Re: Techinal problems with ABF simulations Jérôme Hénin (Wed Jun 27 2012 - 08:29:09 CDT)
jobs with Intel i7 Neelanjana Sengupta (Wed Jun 27 2012 - 07:33:09 CDT)
AW: AW: Atoms moving too fast only with CUDA version. Norman Geist (Wed Jun 27 2012 - 03:28:33 CDT)
- Re: AW: AW: Atoms moving too fast only with CUDA version. amin_at_imtech.res.in (Wed Jun 27 2012 - 09:40:38 CDT)
  - AW: AW: AW: Atoms moving too fast only with CUDA version. Norman Geist (Thu Jun 28 2012 - 00:21:11 CDT)
    - Re: AW: AW: AW: Atoms moving too fast only with CUDA version. amin_at_imtech.res.in (Thu Jun 28 2012 - 01:13:07 CDT)
    - AW: AW: AW: AW: Atoms moving too fast only with CUDA version. Norman Geist (Thu Jun 28 2012 - 02:05:11 CDT)
Atoms moving too fast only with CUDA version. amin_at_imtech.res.in (Wed Jun 27 2012 - 00:37:55 CDT)
- Re: Atoms moving too fast only with CUDA version. Aron Broom (Wed Jun 27 2012 - 00:51:33 CDT)
  - Re: Atoms moving too fast only with CUDA version. amin_at_imtech.res.in (Wed Jun 27 2012 - 01:34:28 CDT)
  - AW: Atoms moving too fast only with CUDA version. Norman Geist (Wed Jun 27 2012 - 01:43:14 CDT)
umbrella sampling ipsita basu (Mon Jun 25 2012 - 02:22:21 CDT)
- Re: umbrella sampling Giacomo Fiorin (Mon Jun 25 2012 - 09:15:50 CDT)
  - Re: umbrella sampling ipsita basu (Tue Jun 26 2012 - 00:13:18 CDT)
    - Re: umbrella sampling koushik.k (Tue Jun 26 2012 - 03:19:23 CDT)
    - Re: umbrella sampling ipsita basu (Tue Jun 26 2012 - 09:49:30 CDT)
  - Re: umbrella sampling Jérôme Hénin (Wed Aug 22 2012 - 05:02:11 CDT)
Nicolas te ha dejado un mensaje... Badoo (Sun Jun 24 2012 - 16:13:10 CDT)
Sudden energy drop after minimization Hyuntae Na (Fri Jun 22 2012 - 19:56:14 CDT)
- AW: Sudden energy drop after minimization Norman Geist (Mon Jun 25 2012 - 00:37:43 CDT)
  - RE: AW: Sudden energy drop after minimization Hyuntae Na (Mon Jun 25 2012 - 00:59:18 CDT)
NAMD 2.9 CUDA multicore, single machine Brett T. Hannigan (Fri Jun 22 2012 - 13:04:34 CDT)
- Re: NAMD 2.9 CUDA multicore, single machine Aron Broom (Fri Jun 22 2012 - 13:49:30 CDT)
  - Re: NAMD 2.9 CUDA multicore, single machine Aron Broom (Fri Jun 22 2012 - 13:49:57 CDT)
AW: GPU cluster Norman Geist (Thu Jun 21 2012 - 05:43:56 CDT)
lookup tables Thomas Brian (Wed Jun 20 2012 - 23:17:11 CDT)
Workshop for Computational Chemistry & Physics MARK PLUMMER (Wed Jun 20 2012 - 15:17:27 CDT)
Fwd: Fwd: Fwd: namd on gtx-680 Francesco Pietra (Wed Jun 20 2012 - 12:57:06 CDT)
- Re: Fwd: Fwd: namd on gtx-680 Axel Kohlmeyer (Wed Jun 20 2012 - 13:52:21 CDT)
  - AW: Fwd: Fwd: namd on gtx-680 Norman Geist (Thu Jun 21 2012 - 00:49:23 CDT)
  - Re: Fwd: Fwd: namd on gtx-680 Francesco Pietra (Thu Jun 21 2012 - 02:10:50 CDT)
    - Re: Fwd: Fwd: namd on gtx-680 Francesco Pietra (Thu Jun 21 2012 - 03:09:27 CDT)
Re: Fwd: Fwd: namd on gtx-680 Francesco Pietra (Wed Jun 20 2012 - 09:38:32 CDT)
- Re: Fwd: Fwd: namd on gtx-680 Vincent Leroux (Wed Jun 20 2012 - 10:03:29 CDT)
- Re: Fwd: Fwd: namd on gtx-680 Axel Kohlmeyer (Wed Jun 20 2012 - 10:11:48 CDT)
Re: Fwd: namd on gtx-680 Francesco Pietra (Wed Jun 20 2012 - 05:08:30 CDT)
- Fwd: Fwd: namd on gtx-680 Francesco Pietra (Wed Jun 20 2012 - 05:10:03 CDT)
- Fwd: Re: Fwd: namd on gtx-680 Francesco Pietra (Wed Jun 20 2012 - 09:06:26 CDT)
ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Robert Johnson (Tue Jun 19 2012 - 15:43:26 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Aron Broom (Tue Jun 19 2012 - 16:56:51 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Jérôme Hénin (Wed Jun 20 2012 - 06:25:36 CDT)
  - Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Robert Johnson (Wed Jun 20 2012 - 11:30:29 CDT)
GPU cluster Matthew B. Roark (Tue Jun 19 2012 - 14:07:58 CDT)
- Re: GPU cluster Axel Kohlmeyer (Tue Jun 19 2012 - 14:40:38 CDT)
  - AW: GPU cluster Norman Geist (Thu Jun 21 2012 - 00:45:48 CDT)
namd simulationâ€‹:protein,lâ€‹igand,lipiâ€‹d,water and ions Marlet Martinez (Tue Jun 19 2012 - 12:33:13 CDT)
- Re: namd simulationâ€‹:protein,lâ€‹igand,lipiâ€‹d,water and ions Aron Broom (Tue Jun 19 2012 - 12:37:13 CDT)
  - Re: Re: namd simulationâ€‹:protein,lâ€‹igand,lipiâ€‹d,water and ions Marlet Martinez (Thu Jun 21 2012 - 09:59:09 CDT)
Problem of 'missing stage' in colvars.state file Shaon Chakrabarti (Tue Jun 19 2012 - 12:15:51 CDT)
- Re: Problem of 'missing stage' in colvars.state file Jérôme Hénin (Wed Jun 20 2012 - 06:32:28 CDT)
  - Re: Problem of 'missing stage' in colvars.state file Jérôme Hénin (Wed Jun 20 2012 - 15:59:20 CDT)
Re: Multi node run causes "CUDA error cudaStreamCreate" Sergei (Tue Jun 19 2012 - 08:32:39 CDT)
- Re: Re: Multi node run causes "CUDA error cudaStreamCreate" Sergei (Fri Jun 22 2012 - 04:36:20 CDT)
mdff error Hamze Rahimi (Mon Jun 18 2012 - 09:41:08 CDT)
Problem running NAMD mpahleva_at_abo.fi (Mon Jun 18 2012 - 01:56:37 CDT)
- Re: Problem running NAMD Nicholas M Glykos (Mon Jun 18 2012 - 02:16:27 CDT)
segmentation errors P Fajer (Sat Jun 16 2012 - 13:14:09 CDT)
Erratic pressure values during equilibration of water box Ashwin C.V. (Sun Jun 17 2012 - 08:49:27 CDT)
- Re: Erratic pressure values during equilibration of water box Axel Kohlmeyer (Sun Jun 17 2012 - 09:08:31 CDT)
[Fwd: Re: FATAL ERROR : Line too long in pdb file] amin_at_imtech.res.in (Fri Jun 15 2012 - 20:25:57 CDT)
- Re: [Fwd: Re: FATAL ERROR : Line too long in pdb file] Aron Broom (Fri Jun 15 2012 - 21:24:20 CDT)
FATAL ERROR : Line too long in pdb file amin_at_imtech.res.in (Fri Jun 15 2012 - 19:43:31 CDT)
- Re: FATAL ERROR : Line too long in pdb file Aron Broom (Fri Jun 15 2012 - 20:10:39 CDT)
memory-optimized version binary coordinates? Carlos Sosa (Fri Jun 15 2012 - 15:43:58 CDT)
- Re: memory-optimized version binary coordinates? Aron Broom (Fri Jun 15 2012 - 16:18:22 CDT)
  - Re: memory-optimized version binary coordinates? Carlos Sosa (Sat Jun 16 2012 - 19:33:36 CDT)
  - Re: memory-optimized version binary coordinates? Carlos Sosa (Mon Jun 25 2012 - 15:06:19 CDT)
Negative surface area? David Minh (Fri Jun 15 2012 - 09:08:12 CDT)
- Re: Negative surface area? David Minh (Tue Jul 24 2012 - 10:36:23 CDT)
  - typo/my flawed thinking on "alchVdwLambdaEnd"? Sebastian Stolzenberg (Tue Sep 04 2012 - 19:20:07 CDT)
    - Re: typo/my flawed thinking on "alchVdwLambdaEnd"? Jérôme Hénin (Wed Sep 05 2012 - 08:13:45 CDT)
running simulations on different machines with different versions of NAMD Puspita Halder (Fri Jun 15 2012 - 01:29:59 CDT)
- Re: running simulations on different machines with different versions of NAMD Aron Broom (Fri Jun 15 2012 - 05:38:20 CDT)
AW: namd simulation:protein,ligand,lipid,water and ions Norman Geist (Fri Jun 15 2012 - 01:20:45 CDT)
minimization and water bubbles Dr. Eddie (Thu Jun 14 2012 - 21:33:27 CDT)
- Re: minimization and water bubbles Axel Kohlmeyer (Thu Jun 14 2012 - 21:49:40 CDT)
  - AW: minimization and water bubbles Norman Geist (Fri Jun 15 2012 - 01:34:42 CDT)
Multiple copy ligand simulations Vijay Vammi (Thu Jun 14 2012 - 13:32:43 CDT)
- Re: Multiple copy ligand simulations JC Gumbart (Thu Jun 14 2012 - 13:42:16 CDT)
  - Re: Multiple copy ligand simulations Vijay Vammi (Thu Jun 14 2012 - 13:48:00 CDT)
could acpype output file be used for NAMD CHARMM FF? Albert (Thu Jun 14 2012 - 13:29:06 CDT)
Buffer Underflow in Multiple Walker MetaDynamics Aron Broom (Thu Jun 14 2012 - 13:26:03 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Giacomo Fiorin (Thu Jun 14 2012 - 13:48:07 CDT)
  - Re: Buffer Underflow in Multiple Walker MetaDynamics Aron Broom (Thu Jun 14 2012 - 14:56:30 CDT)
Re: namd simulation:protein,ligand,lipid,water and ions Marlet Martinez (Thu Jun 14 2012 - 12:29:15 CDT)
Question about optmem input files Carlos Sosa (Thu Jun 14 2012 - 10:33:50 CDT)
Advice on how to perform multiple copy ligand simulation Vijay Vammi (Thu Jun 14 2012 - 08:09:19 CDT)
flipdcd corrupting dcd files peter.schmidtke_at_fr.netgrs.com (Thu Jun 14 2012 - 06:30:48 CDT)
- Re: flipdcd corrupting dcd files Joshua D. Moore (Thu Jun 14 2012 - 13:39:52 CDT)
  - RE: flipdcd corrupting dcd files peter.schmidtke_at_fr.netgrs.com (Fri Jun 15 2012 - 00:58:16 CDT)
    - Re: flipdcd corrupting dcd files Joshua D. Moore (Fri Jun 15 2012 - 09:11:38 CDT)
namd simulation:protein,ligand,lipid,water and ions Marlet Martinez (Wed Jun 13 2012 - 18:44:40 CDT)
- AW: namd simulation:protein,ligand,lipid,water and ions Norman Geist (Thu Jun 14 2012 - 01:50:39 CDT)
making force grids Thomas Brian (Wed Jun 13 2012 - 18:36:00 CDT)
- Re: making force grids Thomas Brian (Wed Jun 20 2012 - 23:08:24 CDT)
  - Re: making force grids Thomas Brian (Fri Jun 22 2012 - 15:37:14 CDT)
Only one process running on cluster amin_at_imtech.res.in (Wed Jun 13 2012 - 02:25:14 CDT)
- AW: Only one process running on cluster Norman Geist (Wed Jun 13 2012 - 03:35:49 CDT)
  - Re: AW: Only one process running on cluster amin_at_imtech.res.in (Wed Jun 13 2012 - 04:02:40 CDT)
    - AW: AW: Only one process running on cluster Norman Geist (Wed Jun 13 2012 - 05:13:45 CDT)
CUDA error on Pe 4: device cannot map host memory Vignesh (Tue Jun 12 2012 - 18:57:14 CDT)
- AW: CUDA error on Pe 4: device cannot map host memory Norman Geist (Wed Jun 13 2012 - 00:58:11 CDT)
  - Re: AW: CUDA error on Pe 4: device cannot map host memory Vignesh (Wed Jun 13 2012 - 02:16:24 CDT)
keeping a protein in a solvation box Dr. Eddie (Tue Jun 12 2012 - 17:44:26 CDT)
- Re: keeping a protein in a solvation box Aaron Oakley (Tue Jun 12 2012 - 18:45:19 CDT)
- Re: keeping a protein in a solvation box Eduard Schreiner (Tue Jun 12 2012 - 18:19:11 CDT)
NAMD-INCONSISTENCY IN SCOR jose correa (Tue Jun 12 2012 - 17:23:00 CDT)
Trying to run a setup with amber force field in NAMD scott davis (Tue Jun 12 2012 - 16:49:55 CDT)
- Re: Trying to run a setup with amber force field in NAMD Aron Broom (Tue Jun 12 2012 - 21:34:09 CDT)
  - Re: Trying to run a setup with amber force field in NAMD johan strumpfer (Thu Jun 14 2012 - 08:18:08 CDT)
- AW: Trying to run a setup with amber force field in NAMD Norman Geist (Wed Jun 13 2012 - 00:50:10 CDT)
- Re: Trying to run a setup with amber force field in NAMD johan strumpfer (Tue Jun 12 2012 - 17:49:46 CDT)
  - AW: Trying to run a setup with amber force field in NAMD Norman Geist (Thu Jun 14 2012 - 01:41:15 CDT)
- Re: Trying to run a setup with amber force field in NAMD Eduard Schreiner (Tue Jun 12 2012 - 18:32:08 CDT)
how to solve such kind of crossterm parameter problem? Liqun Zhang (Tue Jun 12 2012 - 10:28:09 CDT)
- Re: how to solve such kind of crossterm parameter problem? Liqun Zhang (Tue Jun 12 2012 - 10:31:09 CDT)
Targeted Molecular Dynamics Miguel Ángel Mompeán García (Tue Jun 12 2012 - 06:02:17 CDT)
- Re: Targeted Molecular Dynamics harish vashisth (Tue Jun 12 2012 - 11:22:10 CDT)
Force field parameter and topology for zinc finger protein sudipta (Mon Jun 11 2012 - 20:09:56 CDT)
Workshop - Computational Molecular Physics of Non-Bonded Bio-Molecular Interactions MARK PLUMMER (Mon Jun 11 2012 - 17:14:51 CDT)
(no subject) Francesco Pietra (Sun Jun 10 2012 - 12:45:22 CDT)
membrane GPCR-ligands simulations jose correa (Fri Jun 08 2012 - 20:23:46 CDT)
- Re: membrane GPCR-ligands simulations Axel Kohlmeyer (Fri Jun 08 2012 - 20:58:52 CDT)
  - Re: membrane GPCR-ligands simulations Aron Broom (Fri Jun 08 2012 - 21:10:04 CDT)
Query about compressing PSF files Seetha Pothapragada (Fri Jun 08 2012 - 15:44:22 CDT)
please help Adeleke Adebayo Abayomi (Fri Jun 08 2012 - 14:38:18 CDT)
- Re: please help Aron Broom (Fri Jun 08 2012 - 21:13:16 CDT)
using CHARMM22STAR forcefield in NAMD Aaron Oakley (Fri Jun 08 2012 - 03:23:07 CDT)
- Re: using CHARMM22STAR forcefield in NAMD Victor Ovchinnikov (Fri Jun 08 2012 - 09:27:46 CDT)
help on building PATCH Matteo Pappalardo (Fri Jun 08 2012 - 03:15:53 CDT)
AW: compress PSF into INTER Norman Geist (Thu Jun 07 2012 - 05:15:09 CDT)
- Re: AW: compress PSF into INTER JC Gumbart (Thu Jun 07 2012 - 05:26:58 CDT)
  - RE: AW: compress PSF into INTER Cruz-Chu Eduardo Roberto (Thu Jun 07 2012 - 07:02:35 CDT)
cell shape after increasing margin (parm7 ff) Francesco Pietra (Thu Jun 07 2012 - 01:26:35 CDT)
compress PSF into INTER Cruz-Chu Eduardo Roberto (Wed Jun 06 2012 - 13:37:34 CDT)
- AW: compress PSF into INTER Norman Geist (Thu Jun 07 2012 - 01:24:31 CDT)
  - RE: compress PSF into INTER Cruz-Chu Eduardo Roberto (Thu Jun 07 2012 - 04:20:56 CDT)
    - AW: compress PSF into INTER Norman Geist (Thu Jun 07 2012 - 05:11:54 CDT)
pulling force doesn't drop to zero in SMD Luthur Cheung (Tue Jun 05 2012 - 19:06:17 CDT)
pulling force didn't drop to zero in SMD Luthur Cheung (Wed Jun 06 2012 - 08:31:43 CDT)
- Re: pulling force didn't drop to zero in SMD Ajasja LjubetiÄ (Wed Jun 06 2012 - 08:47:35 CDT)
  - Re: pulling force didn't drop to zero in SMD johan strumpfer (Wed Jun 06 2012 - 09:21:23 CDT)
namd/vmd support to GTX-6## series Francesco Pietra (Wed Jun 06 2012 - 03:43:38 CDT)
- Re: vmd-l: namd/vmd support to GTX-6## series John Stone (Wed Jun 06 2012 - 09:13:01 CDT)
  - Re: vmd-l: namd/vmd support to GTX-6## series Francesco Pietra (Thu Jun 21 2012 - 12:36:27 CDT)
Psfgen CTER issues Evgeny Bulat (Tue Jun 05 2012 - 13:00:52 CDT)
FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) Francesco Pietra (Tue Jun 05 2012 - 02:16:40 CDT)
- Re: vmd-l: FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) JC Gumbart (Tue Jun 05 2012 - 09:22:10 CDT)
  - Re: Re: vmd-l: FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) Francesco Pietra (Tue Jun 05 2012 - 12:54:05 CDT)
    - Re: Re: vmd-l: FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) Mayne, Christopher G (Tue Jun 05 2012 - 13:27:13 CDT)
NAMD 2.9 Replica Exchange (+replicas error) Cade Markegard (Mon Jun 04 2012 - 16:57:06 CDT)
- Re: NAMD 2.9 Replica Exchange (+replicas error) Robert Elder (Fri Jul 06 2012 - 13:40:23 CDT)
  - Re: NAMD 2.9 Replica Exchange (+replicas error) Cade Markegard (Fri Jul 06 2012 - 13:56:42 CDT)
RE: charmm to namd conversion Felipe Merino (Mon Jun 04 2012 - 16:39:55 CDT)
Workshop In Aspen Colorado - Molecular Physics of Non-Bonded Biomolecular Interactions MARK PLUMMER (Mon Jun 04 2012 - 15:06:18 CDT)
charmm to namd conversion Matthew B. Roark (Mon Jun 04 2012 - 12:29:55 CDT)
- Re: charmm to namd conversion Felipe Merino (Mon Jun 04 2012 - 13:37:53 CDT)
  - RE: charmm to namd conversion Matthew B. Roark (Wed Jun 06 2012 - 15:40:23 CDT)
    - RE: charmm to namd conversion Felipe Merino (Wed Jun 06 2012 - 16:36:34 CDT)
NOTICE: mail delivery status Jim Phillips (Sun Jun 03 2012 - 23:52:37 CDT)
cuda_check_local_progress polled 1000000 times Francesco Pietra (Sat Jun 02 2012 - 14:06:49 CDT)
- Re: cuda_check_local_progress polled 1000000 times Francesco Pietra (Mon Jun 04 2012 - 12:20:56 CDT)
issue with solute that splits Massimiliano Porrini (Fri Jun 01 2012 - 13:52:45 CDT)
- Re: issue with solute that splits Felipe Merino (Fri Jun 01 2012 - 14:20:22 CDT)
  - Re: issue with solute that splits Aron Broom (Fri Jun 01 2012 - 14:44:37 CDT)
Benefits of SandyBridge EP in NAMD2.9 Florian Mrugalla (Fri Jun 01 2012 - 06:52:19 CDT)
- Re: Benefits of SandyBridge EP in NAMD2.9 Axel Kohlmeyer (Fri Jun 01 2012 - 08:35:37 CDT)
  - Re: Benefits of SandyBridge EP in NAMD2.9 Jérôme Hénin (Fri Jun 01 2012 - 08:57:23 CDT)
    - Re: Benefits of SandyBridge EP in NAMD2.9 Axel Kohlmeyer (Fri Jun 01 2012 - 09:04:52 CDT)
    - Re: Benefits of SandyBridge EP in NAMD2.9 Axel Kohlmeyer (Fri Jun 01 2012 - 09:19:50 CDT)
NAMD fixes for dummy atoms & parameters for divalent metal ions Francesco Pietra (Fri Jun 01 2012 - 03:15:21 CDT)
charmm toppar in namd Matthew B. Roark (Thu May 31 2012 - 14:04:18 CDT)
- Writing an output file into pdb format in a simulation. Ajith Rathnaweera Rajapaksha Mudalige (Thu May 31 2012 - 15:20:58 CDT)
(no subject) Marc Charendoff (Thu May 31 2012 - 12:09:43 CDT)
AW: NAMD feature request Hydrogenscale Norman Geist (Thu May 31 2012 - 01:09:59 CDT)
Breaking of Disulfide Bonds Kapil jain (Wed May 30 2012 - 23:09:25 CDT)
- Re: Breaking of Disulfide Bonds Aron Broom (Wed May 30 2012 - 23:14:21 CDT)
  - Re: Breaking of Disulfide Bonds Gianluca Interlandi (Wed May 30 2012 - 23:29:16 CDT)
- Re: Breaking of Disulfide Bonds Gianluca Interlandi (Wed May 30 2012 - 23:27:20 CDT)
- Re: Breaking of Disulfide Bonds JC Gumbart (Wed May 30 2012 - 23:29:53 CDT)
How to restraint pairinteractions sanxing.xu_at_gmail.com (Wed May 30 2012 - 17:01:20 CDT)
- Re: How to restraint pairinteractions Giacomo Fiorin (Wed May 30 2012 - 17:15:03 CDT)
  - Re: How to restraint pairinteractions Family Xu (Thu May 31 2012 - 11:29:11 CDT)
    - Re: How to restraint pairinteractions Giacomo Fiorin (Fri Jun 01 2012 - 00:20:05 CDT)
Fwd: Three GPU cards on shared-mem motherboard Francesco Pietra (Wed May 30 2012 - 12:33:47 CDT)
- Re: Three GPU cards on shared-mem motherboard Aron Broom (Wed May 30 2012 - 19:50:49 CDT)
  - Re: Three GPU cards on shared-mem motherboard Axel Kohlmeyer (Wed May 30 2012 - 20:02:31 CDT)
    - Re: Three GPU cards on shared-mem motherboard Aron Broom (Wed May 30 2012 - 22:03:24 CDT)
  - Re: Three GPU cards on shared-mem motherboard Francesco Pietra (Thu May 31 2012 - 00:53:33 CDT)
    - Re: Three GPU cards on shared-mem motherboard Aron Broom (Fri Jun 01 2012 - 10:34:58 CDT)
question about dcd file Hasan haska (Wed May 30 2012 - 07:22:11 CDT)
- Re: question about dcd file Cesar Millan (Wed May 30 2012 - 07:39:21 CDT)
- Re: question about dcd file Chiara Cosenza unina (Wed May 30 2012 - 07:40:27 CDT)
Re: NAMD feature request Hydrogenscale Axel Kohlmeyer (Wed May 30 2012 - 04:20:03 CDT)
- Re: NAMD feature request Hydrogenscale Ajasja LjubetiÄ (Wed May 30 2012 - 06:16:46 CDT)
  - Re: NAMD feature request Hydrogenscale Jérôme Hénin (Wed May 30 2012 - 06:51:47 CDT)
  - Re: NAMD feature request Hydrogenscale Axel Kohlmeyer (Wed May 30 2012 - 07:14:40 CDT)
NAMD feature request Hydrogenscale Norman Geist (Wed May 30 2012 - 02:36:16 CDT)
about trajectory analysis oguz gurbulak (Wed May 30 2012 - 01:43:42 CDT)
- Re: about trajectory analysis Nicholas M Glykos (Wed May 30 2012 - 02:06:56 CDT)
- AW: about trajectory analysis Norman Geist (Wed May 30 2012 - 02:18:25 CDT)
About the correction of charging two ion water box by using FEP Win Liu (Mon May 28 2012 - 11:59:33 CDT)
- Re: About the correction of charging two ion water box by using FEP JC Gumbart (Mon May 28 2012 - 17:15:35 CDT)
  - Re: About the correction of charging two ion water box by using FEP Win Liu (Sat Jun 02 2012 - 03:34:28 CDT)
    - RE: About the correction of charging two ion water box by using FEP JC Gumbart (Sat Jun 02 2012 - 07:43:15 CDT)
Three GPU cards on shared-mem motherboard Francesco Pietra (Mon May 28 2012 - 03:53:02 CDT)
- Re: Three GPU cards on shared-mem motherboard Axel Kohlmeyer (Mon May 28 2012 - 05:35:51 CDT)
  - Re: Three GPU cards on shared-mem motherboard Francesco Pietra (Mon May 28 2012 - 11:03:43 CDT)
  - Re: Three GPU cards on shared-mem motherboard Francesco Pietra (Wed May 30 2012 - 02:45:24 CDT)
    - Re: Three GPU cards on shared-mem motherboard Aron Broom (Wed May 30 2012 - 09:14:17 CDT)
    - Re: Three GPU cards on shared-mem motherboard Francesco Pietra (Wed May 30 2012 - 10:33:14 CDT)
- AW: Three GPU cards on shared-mem motherboard Norman Geist (Tue May 29 2012 - 01:24:34 CDT)
About the correction of charging two ion water box by using FEP Win Liu (Mon May 28 2012 - 02:06:09 CDT)
- RE: About the correction of charging two ion water box by using FEP JC Gumbart (Mon May 28 2012 - 08:41:56 CDT)
protein folding by simulated anneling Puspita Halder (Mon May 28 2012 - 01:11:53 CDT)
- Re: protein folding by simulated anneling Aron Broom (Mon May 28 2012 - 08:55:11 CDT)
AW: AW: Generating force field for novel molecules Norman Geist (Fri May 25 2012 - 00:56:07 CDT)
- Re: AW: AW: Generating force field for novel molecules Sajad Falsafi-Zadeh (Fri May 25 2012 - 01:50:35 CDT)
  - Re: AW: AW: Generating force field for novel molecules Axel Kohlmeyer (Fri May 25 2012 - 05:44:42 CDT)
- Re: AW: AW: Generating force field for novel molecules Jeffrey Potoff (Fri May 25 2012 - 09:34:11 CDT)
- Re: AW: AW: Generating force field for novel molecules Mayne, Christopher G (Fri May 25 2012 - 12:07:43 CDT)
queries about "Tclforces" utility in NAMD harish vashisth (Fri May 25 2012 - 00:06:28 CDT)
- AW: queries about "Tclforces" utility in NAMD Norman Geist (Fri May 25 2012 - 01:11:47 CDT)
- Re: queries about "Tclforces" utility in NAMD Jérôme Hénin (Fri May 25 2012 - 02:48:01 CDT)
Advertisement Workshop Aspen Center for Physics MARK PLUMMER (Thu May 24 2012 - 16:04:35 CDT)
Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Benjamin Merget (Thu May 24 2012 - 04:51:06 CDT)
- AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Norman Geist (Fri May 25 2012 - 01:10:17 CDT)
  - Re: AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Benjamin Merget (Sun May 27 2012 - 09:04:48 CDT)
    - AW: AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Norman Geist (Tue May 29 2012 - 00:59:55 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Axel Kohlmeyer (Fri May 25 2012 - 05:39:37 CDT)
  - Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Benjamin Merget (Sun May 27 2012 - 09:10:59 CDT)
hbonds colvar component Vlad Cojocaru (Thu May 24 2012 - 02:13:29 CDT)
- Re: hbonds colvar component Giacomo Fiorin (Thu May 24 2012 - 08:58:04 CDT)
  - Re: hbonds colvar component Vlad Cojocaru (Thu May 24 2012 - 09:47:45 CDT)
    - Re: hbonds colvar component Giacomo Fiorin (Thu May 24 2012 - 10:12:51 CDT)
protein folding by simulated annealing method Puspita Halder (Thu May 24 2012 - 00:01:25 CDT)
Issues with 'Gyration' in Colvars module Shaon Chakrabarti (Wed May 23 2012 - 14:48:35 CDT)
- Re: Issues with 'Gyration' in Colvars module Aron Broom (Wed May 23 2012 - 14:56:49 CDT)
  - Re: Issues with 'Gyration' in Colvars module Giacomo Fiorin (Wed May 23 2012 - 15:27:51 CDT)
(no subject) Puspita Halder (Wed May 23 2012 - 07:45:48 CDT)
Generating force field for novel molecules MOHAMMAD JAVAD AGHAEI (Wed May 23 2012 - 03:16:36 CDT)
- AW: Generating force field for novel molecules Norman Geist (Thu May 24 2012 - 00:15:11 CDT)
TMD output format Payne, Christy (Mon May 21 2012 - 10:00:24 CDT)
- Re: TMD output format JC Gumbart (Mon May 21 2012 - 11:34:17 CDT)
Parameters for Cesium Burgess, Don E (Thu May 17 2012 - 11:43:44 CDT)
FEP - Dynamic charges John Baker (Tue May 15 2012 - 12:38:59 CDT)
- AW: FEP - Dynamic charges Norman Geist (Wed May 16 2012 - 00:48:20 CDT)
- Re: FEP - Dynamic charges Jérôme Hénin (Wed May 16 2012 - 03:03:54 CDT)
MDFF for protein complex Hamze Rahimi (Mon May 14 2012 - 09:22:42 CDT)
- MDFF for huge trajectories Samuel Flores (Wed May 16 2012 - 14:31:53 CDT)
  - Re: MDFF for huge trajectories Ajasja LjubetiÄ (Wed May 16 2012 - 16:36:41 CDT)
    - Re: MDFF for huge trajectories Samuel Flores (Wed May 16 2012 - 17:20:29 CDT)
    - Re: MDFF for huge trajectories Samuel Flores (Wed May 16 2012 - 17:54:56 CDT)
five 'ERROR' in the log file of NAMD2.9 ypg (Sun May 13 2012 - 02:15:27 CDT)
- RE: five 'ERROR' in the log file of NAMD2.9 JC Gumbart (Sun May 13 2012 - 08:23:53 CDT)
- RE: five 'ERROR' in the log file of NAMD2.9 ypg (Sun May 13 2012 - 09:13:49 CDT)
Problem with Methane-Methane PMF Shaon Chakrabarti (Fri May 11 2012 - 16:08:23 CDT)
- Re: Problem with Methane-Methane PMF Aron Broom (Fri May 11 2012 - 16:38:03 CDT)
- Re: Problem with Methane-Methane PMF Giacomo Fiorin (Fri May 11 2012 - 16:40:03 CDT)
  - Re: Problem with Methane-Methane PMF Shaon Chakrabarti (Sat May 12 2012 - 13:46:01 CDT)
Atomic Radii for GB Implicit Solvent Aron Broom (Fri May 11 2012 - 14:40:12 CDT)
fixed bond length Mortaza Aghtar (Fri May 11 2012 - 10:51:01 CDT)
- Re: fixed bond length Ajasja LjubetiÄ (Fri May 11 2012 - 11:06:35 CDT)
  - Re: fixed bond length Mortaza Aghtar (Fri May 11 2012 - 11:29:12 CDT)
    - Re: fixed bond length Aron Broom (Fri May 11 2012 - 13:25:14 CDT)
    - AW: fixed bond length Norman Geist (Mon May 14 2012 - 01:23:05 CDT)
Multicore executable error Caitlin Scott (Wed May 09 2012 - 13:05:20 CDT)
- Re: Multicore executable error Chris Harrison (Wed May 09 2012 - 16:21:02 CDT)
Fwd: AW: stereo-chemical inversion during MD Gordon Wells (Wed May 09 2012 - 10:04:04 CDT)
Fwd: Re: AW: stereo-chemical inversion during MD Branko (Tue May 08 2012 - 03:26:25 CDT)
- Re: Re: AW: stereo-chemical inversion during MD Axel Kohlmeyer (Tue May 08 2012 - 08:33:03 CDT)
  - Re: AW: stereo-chemical inversion during MD Branko (Tue May 08 2012 - 10:51:46 CDT)
Fwd: stereo-chemical inversion during MD Francesco Pietra (Tue May 08 2012 - 01:59:49 CDT)
stereo-chemical inversion during MD Gordon Wells (Mon May 07 2012 - 12:01:24 CDT)
- AW: stereo-chemical inversion during MD Norman Geist (Tue May 08 2012 - 01:01:05 CDT)
  - Re: AW: stereo-chemical inversion during MD Branko (Tue May 08 2012 - 15:03:08 CDT)
- Re: stereo-chemical inversion during MD Branko (Tue May 08 2012 - 04:53:27 CDT)
Specific colvar component needed. Germán Andrés Miño (Mon May 07 2012 - 10:55:14 CDT)
- Re: Specific colvar component needed. Aron Broom (Mon May 07 2012 - 11:02:30 CDT)
  - Re: Specific colvar component needed. Giacomo Fiorin (Mon May 07 2012 - 11:05:41 CDT)
Hole Buddhadev Maiti (Fri May 04 2012 - 22:47:27 CDT)
Fwd: Re: charmrun setup Branko (Sat May 05 2012 - 13:37:05 CDT)
- AW: Re: charmrun setup Norman Geist (Mon May 07 2012 - 00:49:22 CDT)
charmrun setup Pedro Armando Ojeda May (Sat May 05 2012 - 13:14:12 CDT)
Applying TclBC script every x steps Error Maria Pikoula (Fri May 04 2012 - 16:46:03 CDT)
Concerning Restarting Multiple Walkers MetaDynamics Aron Broom (Fri May 04 2012 - 15:52:41 CDT)
- Re: Concerning Restarting Multiple Walkers MetaDynamics Aron Broom (Fri May 04 2012 - 15:54:28 CDT)
  - Re: Re: Concerning Restarting Multiple Walkers MetaDynamics Giacomo Fiorin (Fri May 04 2012 - 16:30:26 CDT)
    - Re: Re: Concerning Restarting Multiple Walkers MetaDynamics Aron Broom (Fri May 04 2012 - 16:33:39 CDT)
A question about the CHARMM force field Hall McDull (Fri May 04 2012 - 03:32:30 CDT)
- A question about the CHARMM force field Hall McDull (Fri May 04 2012 - 07:33:48 CDT)
  - Re: A question about the CHARMM force field Axel Kohlmeyer (Fri May 04 2012 - 08:12:26 CDT)
Umbrella sampling-reliability of results Parisa Akhski (Fri May 04 2012 - 09:20:17 CDT)
- Re: Umbrella sampling-reliability of results Aron Broom (Fri May 04 2012 - 09:41:35 CDT)
Periodic cell has become too small lecan (Fri May 04 2012 - 00:19:38 CDT)
forces saved in forcedcd Xiaohu Li (Thu May 03 2012 - 15:43:50 CDT)
- Re: forces saved in forcedcd Chris Harrison (Thu May 03 2012 - 18:42:19 CDT)
  - Re: forces saved in forcedcd Xiaohu Li (Thu May 03 2012 - 19:51:36 CDT)
NAMD 2.9 released Jim Phillips (Thu May 03 2012 - 10:27:09 CDT)
Need help preventing hydration of the lipid-protein interface in my system Syed Kashif Zafar (Thu May 03 2012 - 05:48:48 CDT)
- Re: Need help preventing hydration of the lipid-protein interface in my system Chris Harrison (Thu May 03 2012 - 18:31:50 CDT)
a question about ensemble Albert (Thu May 03 2012 - 01:04:58 CDT)
tclBC incorrect output P.-L. Chau (Wed May 02 2012 - 22:18:21 CDT)
- AW: tclBC incorrect output Norman Geist (Thu May 03 2012 - 00:55:58 CDT)
  - Re: AW: tclBC incorrect output P.-L. Chau (Thu May 03 2012 - 01:44:17 CDT)
Question about targetsNumSteps in ColVar Wang Yi (Wed May 02 2012 - 08:52:26 CDT)
- Re: Question about targetsNumSteps in ColVar Giacomo Fiorin (Wed May 02 2012 - 11:38:18 CDT)
  - Re: Question about targetsNumSteps in ColVar Wang Yi (Wed May 02 2012 - 11:54:20 CDT)
    - Re: Question about targetsNumSteps in ColVar Giacomo Fiorin (Wed May 02 2012 - 11:57:34 CDT)
    - Re: Question about targetsNumSteps in ColVar Wang Yi (Wed May 02 2012 - 12:05:16 CDT)
ion placement method vs total energy of the system raghav singh (Mon Apr 30 2012 - 10:25:42 CDT)
- Re: ion placement method vs total energy of the system Anurag Sethi (Mon Apr 30 2012 - 10:36:59 CDT)
non integral charges raghav singh (Mon Apr 30 2012 - 08:06:15 CDT)
- Re: non integral charges Branko (Mon Apr 30 2012 - 08:24:29 CDT)
nucleic acids - total charge raghav singh (Mon Apr 30 2012 - 04:55:38 CDT)
- Re: nucleic acids - total charge Boyang Wang (Tue May 01 2012 - 02:50:35 CDT)
  - Re: nucleic acids - total charge Axel Kohlmeyer (Tue May 01 2012 - 07:37:18 CDT)
- Re: nucleic acids - total charge JC Gumbart (Tue May 01 2012 - 10:48:19 CDT)
  - Re: nucleic acids - total charge Raghav (Tue May 01 2012 - 11:18:22 CDT)
    - Re: nucleic acids - total charge JC Gumbart (Tue May 01 2012 - 11:34:48 CDT)
AW: AW: Set up NPT simulation in cubic PBC-box Norman Geist (Mon Apr 30 2012 - 00:29:21 CDT)
AW: AW: Set up NPT simulation in cubic PBC-box Norman Geist (Mon Apr 30 2012 - 00:21:02 CDT)
non integer total charge raghav singh (Sat Apr 28 2012 - 21:16:02 CDT)
- Re: non integer total charge Chris Harrison (Sat Apr 28 2012 - 21:23:42 CDT)
fwd: sara (Fri Apr 27 2012 - 21:51:50 CDT)
fwd: sara (Fri Apr 27 2012 - 21:51:49 CDT)
Go model in NAMD? Bin Zhang (Thu Apr 26 2012 - 16:52:26 CDT)
Set up NPT simulation in cubic PBC-box Xi Cheng (Thu Apr 26 2012 - 16:22:33 CDT)
- AW: Set up NPT simulation in cubic PBC-box Norman Geist (Fri Apr 27 2012 - 00:42:29 CDT)
  - Re: AW: Set up NPT simulation in cubic PBC-box Xi Cheng (Fri Apr 27 2012 - 10:22:56 CDT)
  - Re: AW: Set up NPT simulation in cubic PBC-box Aron Broom (Mon Apr 30 2012 - 01:40:35 CDT)
- Re: Set up NPT simulation in cubic PBC-box Axel Kohlmeyer (Fri Apr 27 2012 - 10:54:15 CDT)
  - Re: Set up NPT simulation in cubic PBC-box Xi Cheng (Fri Apr 27 2012 - 11:08:42 CDT)
    - Re: Set up NPT simulation in cubic PBC-box Axel Kohlmeyer (Fri Apr 27 2012 - 11:11:30 CDT)
GPCR MD Tutorial Anirban Ghosh (Thu Apr 26 2012 - 04:18:08 CDT)
constant pulling velocity in SMD Jiao, Dian NMN (-EXP) (Wed Apr 25 2012 - 14:41:06 CDT)
- Re: constant pulling velocity in SMD Axel Kohlmeyer (Wed Apr 25 2012 - 17:16:15 CDT)
- constant pulling velocity in SMD Jiao, Dian NMN (-EXP) (Thu Apr 26 2012 - 11:33:07 CDT)
  - Re: constant pulling velocity in SMD JC Gumbart (Thu Apr 26 2012 - 18:15:42 CDT)
About error in .pgn error in vmd cmd prompt Vidhya Sankar (Wed Apr 25 2012 - 03:00:33 CDT)
In-Residence Training at the Theoretical & Computational Biophysics Group, July 16-27, 2012 TCBG Workshop (Tue Apr 24 2012 - 14:06:22 CDT)
- Martini parameter files Chiara Cosenza unina (Thu Apr 26 2012 - 04:45:18 CDT)
FEP using amber topologies felmerino_at_uchile.cl (Mon Apr 23 2012 - 17:46:17 CDT)
Question about GPUs hardware. Cesar Millan (Mon Apr 23 2012 - 17:32:01 CDT)
- Re: Question about GPUs hardware. Aron Broom (Mon Apr 23 2012 - 17:57:56 CDT)
  - Re: Question about GPUs hardware. Aron Broom (Mon Apr 23 2012 - 19:51:44 CDT)
  - AW: Question about GPUs hardware. Norman Geist (Tue Apr 24 2012 - 01:11:01 CDT)
FEP difficulties between two ion species Jeremy Parlin (Mon Apr 23 2012 - 16:38:31 CDT)
- Re: FEP difficulties between two ion species Jérôme Hénin (Tue Apr 24 2012 - 07:19:45 CDT)
  - Re: FEP difficulties between two ion species Niklaus Johner (Fri May 18 2012 - 09:13:06 CDT)
    - Re: FEP difficulties between two ion species Jérôme Hénin (Sat May 19 2012 - 15:11:55 CDT)
    - Re: FEP difficulties between two ion species Jérôme Hénin (Wed May 23 2012 - 13:21:26 CDT)
AW: vmd-l: segmentation fault with NAMDenergy Norman Geist (Mon Apr 23 2012 - 00:52:17 CDT)
AW: problem with gpu namd 2.9b3 Norman Geist (Mon Apr 23 2012 - 00:45:58 CDT)
- Re: problem with gpu namd 2.9b3 Peter Jones (Mon Apr 23 2012 - 01:00:11 CDT)
(no subject) Taruna Gupta (Sun Apr 22 2012 - 12:37:42 CDT)
- Re: Axel Kohlmeyer (Sun Apr 22 2012 - 12:49:15 CDT)
  - Re: Aron Broom (Sun Apr 22 2012 - 16:07:24 CDT)
Simulation Using Both NAMD and VMD Ajith Rathnaweera Rajapaksha Mudalige (Fri Apr 20 2012 - 17:05:28 CDT)
- Re: Simulation Using Both NAMD and VMD Axel Kohlmeyer (Fri Apr 20 2012 - 17:10:30 CDT)
  - Re: Simulation Using Both NAMD and VMD Aron Broom (Fri Apr 20 2012 - 17:30:14 CDT)
Bug with BOUNDARY energy in postprocessing? David Minh (Fri Apr 20 2012 - 13:03:31 CDT)
- Re: Bug with BOUNDARY energy in postprocessing? David Minh (Fri Apr 20 2012 - 13:10:29 CDT)
  - Re: Re: Bug with BOUNDARY energy in postprocessing? Chris Harrison (Fri Apr 20 2012 - 19:41:37 CDT)
Re: problem with gpu namd 2.9b3 Aron Broom (Fri Apr 20 2012 - 09:25:40 CDT)
What is the means of system-min.conf in the Residue-Based Coarse tutorial? javacfish (Fri Apr 20 2012 - 01:17:57 CDT)
- Re: What is the means of system-min.conf in the Residue-Based Coarse tutorial? Ramya Gamini (Fri Apr 20 2012 - 14:32:41 CDT)
segmentation fault with NAMDenergy amin_at_imtech.res.in (Thu Apr 19 2012 - 10:19:55 CDT)
- AW: segmentation fault with NAMDenergy Norman Geist (Fri Apr 20 2012 - 01:00:23 CDT)
problem with gpu namd 2.9b3 Peter Jones (Thu Apr 19 2012 - 04:30:42 CDT)
- AW: problem with gpu namd 2.9b3 Norman Geist (Fri Apr 20 2012 - 00:45:50 CDT)
Using Measure SASA in NAMD Simulations Ajith Rathnaweera Rajapaksha Mudalige (Mon Apr 16 2012 - 20:22:28 CDT)
- Re: Using Measure SASA in NAMD Simulations Aron Broom (Tue Apr 17 2012 - 02:02:16 CDT)
Amber topology felmerino_at_uchile.cl (Mon Apr 16 2012 - 16:13:54 CDT)
creating a protonated cytidine entry raghav singh (Mon Apr 16 2012 - 06:35:15 CDT)
psfgen warnings Vidhya Sankar (Sun Apr 15 2012 - 01:27:14 CDT)
- Re: psfgen warnings Syed Kashif Zafar (Sun Apr 15 2012 - 23:28:49 CDT)
- RE: psfgen warnings hannes.loeffler_at_stfc.ac.uk (Mon Apr 16 2012 - 02:35:35 CDT)
Abouf Psfgen error Syed Kashif Zafar (Sat Apr 14 2012 - 14:50:37 CDT)
About psfgen error Vidhya Sankar (Sat Apr 14 2012 - 11:15:01 CDT)
namd and x-plor Hasan haska (Sat Apr 14 2012 - 06:19:57 CDT)
- Re: namd and x-plor Jernej Zidar (Sat Apr 14 2012 - 08:16:08 CDT)
About error during creation of psf file Vidhya Sankar (Sat Apr 14 2012 - 01:28:27 CDT)
- Re: About error during creation of psf file flavio seixas (Thu Apr 19 2012 - 13:48:42 CDT)
(no subject) Vidhya Sankar (Sat Apr 14 2012 - 01:26:21 CDT)
- (no subject) Hannes Loeffler (Mon Apr 16 2012 - 03:34:41 CDT)
- (no subject) David Rogers (Wed Apr 18 2012 - 23:21:43 CDT)
about molecular axis Namd Namd (Wed Apr 11 2012 - 05:40:30 CDT)
fatal error running namd on Mac Jiao, Dian NMN (-EXP) (Tue Apr 10 2012 - 17:53:54 CDT)
- Re: fatal error running namd on Mac Aron Broom (Tue Apr 10 2012 - 18:04:25 CDT)
  - Re: fatal error running namd on Mac JC Gumbart (Tue Apr 10 2012 - 20:25:46 CDT)
  - Re: fatal error running namd on Mac johan strumpfer (Tue Apr 10 2012 - 19:05:26 CDT)
Importing a DCD into Mathematica Ajasja LjubetiÄ (Tue Apr 10 2012 - 14:58:30 CDT)
- Re: Importing a DCD into Mathematica Branko (Tue Apr 10 2012 - 15:09:51 CDT)
  - Re: Importing a DCD into Mathematica Ajasja LjubetiÄ (Tue Apr 10 2012 - 16:38:24 CDT)
User-defined forces in NAMD Ali Ghaffaari (Tue Apr 10 2012 - 06:38:13 CDT)
- Re: User-defined forces in NAMD Axel Kohlmeyer (Tue Apr 10 2012 - 07:16:18 CDT)
  - Re: User-defined forces in NAMD Ehsan Ban (Tue Apr 10 2012 - 11:55:30 CDT)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE AUC Kiarash Hosseini (Tue Apr 10 2012 - 04:24:10 CDT)
NAMD 2.9b3 colvars oddity Aron Broom (Mon Apr 09 2012 - 20:48:32 CDT)
- Re: NAMD 2.9b3 colvars oddity Giacomo Fiorin (Tue Apr 10 2012 - 16:54:39 CDT)
how to generate psf for membrane+protein Jiao, Dian NMN (-EXP) (Mon Apr 09 2012 - 18:16:59 CDT)
Nonzero BOUNDARY ENERGY without periodic boundary conditions David Minh (Mon Apr 09 2012 - 12:36:25 CDT)
- Re: Nonzero BOUNDARY ENERGY without periodic boundary conditions JC Gumbart (Mon Apr 09 2012 - 18:27:33 CDT)
  - Re: Nonzero BOUNDARY ENERGY without periodic boundary conditions David Minh (Tue Apr 10 2012 - 08:35:37 CDT)
Galilean Invariant Thermostat Ismail, Mohd F. (Sun Apr 08 2012 - 18:26:38 CDT)
- Re: Galilean Invariant Thermostat Jérôme Hénin (Mon Apr 09 2012 - 04:43:37 CDT)
Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort. Nikolaos Glykos (Sun Apr 08 2012 - 12:25:15 CDT)
- Re: Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort. Axel Kohlmeyer (Sun Apr 08 2012 - 12:38:10 CDT)
  - Re: Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort. Nikolaos Glykos (Sun Apr 08 2012 - 13:08:59 CDT)
Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved) Thomas Albers (Sat Apr 07 2012 - 16:44:35 CDT)
- Re: Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved) Jim Phillips (Fri Apr 27 2012 - 14:10:20 CDT)
  - Re: Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved) Thomas Albers (Sun Apr 29 2012 - 08:33:54 CDT)
NAMD 2.9b3 released Jim Phillips (Fri Apr 06 2012 - 08:38:23 CDT)
multicore versus net-linux Gianluca Interlandi (Thu Apr 05 2012 - 20:04:57 CDT)
- Re: multicore versus net-linux Jim Phillips (Thu Apr 05 2012 - 22:40:09 CDT)
  - AW: multicore versus net-linux Norman Geist (Wed Apr 11 2012 - 01:05:33 CDT)
  - Re: multicore versus net-linux Chris Harrison (Fri Apr 20 2012 - 19:46:56 CDT)
DCD Buddhadev Maiti (Thu Apr 05 2012 - 15:44:43 CDT)
- Re: DCD Gianluca Interlandi (Thu Apr 05 2012 - 16:04:41 CDT)
  - RE: DCD Buddhadev Maiti (Thu Apr 05 2012 - 16:22:52 CDT)
  - Re: DCD Ernesto Vargas (Thu Apr 05 2012 - 16:21:19 CDT)
changing harmonic restraints (colvars) Jon Phillips (Thu Apr 05 2012 - 06:52:46 CDT)
- Re: changing harmonic restraints (colvars) Aron Broom (Thu Apr 05 2012 - 10:01:16 CDT)
  - Re: changing harmonic restraints (colvars) Jérôme Hénin (Thu Apr 05 2012 - 11:17:56 CDT)
Re: Line minimizerfailure because of IMPR? Francesco Pietra (Thu Apr 05 2012 - 03:57:03 CDT)
AW: Line minimizerfailure because of IMPR? Norman Geist (Thu Apr 05 2012 - 03:24:12 CDT)
Fwd: Line minimizerfailure because of IMPR? Francesco Pietra (Thu Apr 05 2012 - 03:02:14 CDT)
- Fwd: Line minimizerfailure because of IMPR? Francesco Pietra (Thu Apr 05 2012 - 03:10:59 CDT)
- AW: Line minimizerfailure because of IMPR? Norman Geist (Thu Apr 05 2012 - 03:28:14 CDT)
how to edit restart.coor Jiao, Dian NMN (-EXP) (Wed Apr 04 2012 - 17:29:26 CDT)
- Re: how to edit restart.coor Aron Broom (Wed Apr 04 2012 - 17:47:52 CDT)
  - Re: [EXTERNAL] Re: how to edit restart.coor Jiao, Dian NMN (-EXP) (Wed Apr 04 2012 - 17:56:38 CDT)
  - AW: how to edit restart.coor Norman Geist (Thu Apr 05 2012 - 01:18:58 CDT)
MetaDynamics in 2.9b2 Question Aron Broom (Wed Apr 04 2012 - 14:54:39 CDT)
- Re: MetaDynamics in 2.9b2 Question Giacomo Fiorin (Wed Apr 04 2012 - 19:32:41 CDT)
  - Re: MetaDynamics in 2.9b2 Question Aron Broom (Wed Apr 04 2012 - 20:24:56 CDT)
  - Re: MetaDynamics in 2.9b2 Question Robert Elder (Fri Nov 09 2012 - 11:17:41 CST)
    - Re: MetaDynamics in 2.9b2 Question Aron Broom (Fri Nov 09 2012 - 11:32:53 CST)
    - Re: MetaDynamics in 2.9b2 Question Giacomo Fiorin (Fri Nov 09 2012 - 11:38:10 CST)
CUDA problem? Albert (Wed Apr 04 2012 - 14:02:49 CDT)
- CUDA problem with 2.9b2 Albert (Thu Apr 05 2012 - 00:51:05 CDT)
- AW: CUDA problem? Norman Geist (Thu Apr 05 2012 - 01:12:24 CDT)
  - Re: AW: CUDA problem? Albert (Thu Apr 05 2012 - 01:15:52 CDT)
Line minimizerfailure because of IMPR? Francesco Pietra (Wed Apr 04 2012 - 10:01:45 CDT)
- AW: Line minimizerfailure because of IMPR? Norman Geist (Thu Apr 05 2012 - 01:08:31 CDT)
mdff energy calculation snoze pa (Mon Apr 02 2012 - 10:56:28 CDT)
Protonated nucleotides Zack Scholl (Mon Apr 02 2012 - 07:49:53 CDT)
- Re: Protonated nucleotides johan strumpfer (Mon Apr 02 2012 - 11:15:50 CDT)
  - Re: Protonated nucleotides Aksimentiev, Oleksii (Mon Apr 02 2012 - 13:45:27 CDT)
    - Re: Protonated nucleotides Zack Scholl (Wed Apr 04 2012 - 16:02:22 CDT)
psfgen tyrosine anion-Fe bond Francesco Pietra (Sun Apr 01 2012 - 09:53:13 CDT)
- Re: psfgen tyrosine anion-Fe bond Francesco Pietra (Sun Apr 01 2012 - 12:03:17 CDT)
  - Re: psfgen tyrosine anion-Fe bond Francesco Pietra (Sun Apr 01 2012 - 12:14:27 CDT)
NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 Thomas Albers (Sat Mar 31 2012 - 18:00:06 CDT)
- Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 Nicholas M Glykos (Sun Apr 01 2012 - 03:41:08 CDT)
Bug in SASA for alanin example John Jumper (Fri Mar 30 2012 - 15:10:44 CDT)
Dielectric constant for MDFF of a membrane protein. Raul Araya (Fri Mar 30 2012 - 09:18:22 CDT)
- Re: Dielectric constant for MDFF of a membrane protein. JC Gumbart (Fri Mar 30 2012 - 13:55:56 CDT)
Compiling NAMD_2.9b2_Source with GCC 4.7.0 Fabien Archambault (Fri Mar 30 2012 - 08:25:18 CDT)
- Re: Compiling NAMD_2.9b2_Source with GCC 4.7.0 Axel Kohlmeyer (Fri Mar 30 2012 - 08:32:19 CDT)
- Re: Compiling NAMD_2.9b2_Source with GCC 4.7.0 Jim Phillips (Fri Mar 30 2012 - 10:21:21 CDT)
CHARMM-GUI running error for ligand Hannes Loeffler (Fri Mar 30 2012 - 05:39:17 CDT)
CHARMM-GUI running error for ligand Albert (Fri Mar 30 2012 - 02:37:10 CDT)
- Re: CHARMM-GUI running error for ligand Chiara Cosenza unina (Fri Mar 30 2012 - 05:05:58 CDT)
  - Re: CHARMM-GUI running error for ligand Albert (Fri Mar 30 2012 - 05:27:35 CDT)
  - Re: CHARMM-GUI running error for ligand Albert (Fri Mar 30 2012 - 05:48:12 CDT)
    - Re: CHARMM-GUI running error for ligand Hannes Loeffler (Fri Mar 30 2012 - 05:50:58 CDT)
The simplest pair list generation scheme anaome_at_fundp.ac.be (Thu Mar 29 2012 - 14:01:45 CDT)
PDB sugar unit residue name Massimiliano Porrini (Thu Mar 29 2012 - 06:03:40 CDT)
- Re: PDB sugar unit residue name Aron Broom (Thu Mar 29 2012 - 07:52:20 CDT)
- Re: PDB sugar unit residue name Michelle Kuttel (Thu Mar 29 2012 - 09:30:25 CDT)
  - Re: PDB sugar unit residue name Olgun Guvench (Thu Mar 29 2012 - 11:14:52 CDT)
GBIS and thermostats Gianluca Interlandi (Wed Mar 28 2012 - 21:48:40 CDT)
output nonbonded and bonded terms separately chris liopiri (Wed Mar 28 2012 - 04:59:36 CDT)
collective variable component -- eigenvector usage chang (Tue Mar 27 2012 - 19:46:04 CDT)
- Re: collective variable component -- eigenvector usage Giacomo Fiorin (Tue Mar 27 2012 - 21:13:00 CDT)
NAMD 2.9b2 released Jim Phillips (Tue Mar 27 2012 - 15:17:30 CDT)
2.9b1 crashes Francesco Pietra (Tue Mar 27 2012 - 09:56:15 CDT)
- Re: 2.9b1 crashes Chris Harrison (Tue Mar 27 2012 - 10:15:36 CDT)
  - Re: 2.9b1 crashes Chris Harrison (Tue Mar 27 2012 - 20:33:25 CDT)
  - Re: 2.9b1 crashes Chris Harrison (Wed Mar 28 2012 - 15:41:39 CDT)
Re: How to Get Bonded Pair Force Calculation with NAMD Ehsan Ban (Tue Mar 27 2012 - 09:01:04 CDT)
- AW: How to Get Bonded Pair Force Calculation with NAMD Norman Geist (Wed Mar 28 2012 - 01:11:34 CDT)
AW: AW: conf file question Norman Geist (Mon Mar 26 2012 - 00:39:38 CDT)
How to Get Bonded Pair Force Calculation with NAMD Ehsan Ban (Mon Mar 26 2012 - 07:41:01 CDT)
- AW: How to Get Bonded Pair Force Calculation with NAMD Norman Geist (Tue Mar 27 2012 - 01:16:10 CDT)
accelMD parameter choice Grant Schauer (Sat Mar 24 2012 - 17:08:55 CDT)
- Re: accelMD parameter choice Chris Harrison (Sat Mar 24 2012 - 17:23:50 CDT)
AW: conf file question Norman Geist (Fri Mar 23 2012 - 06:09:41 CDT)
Nonbonded 3-body potential Xavier Bidault (Fri Mar 23 2012 - 05:44:59 CDT)
- Re: Nonbonded 3-body potential Axel Kohlmeyer (Fri Mar 23 2012 - 06:39:52 CDT)
Umbrella sampling with hbond Payne, Christy (Thu Mar 22 2012 - 19:05:24 CDT)
- Re: Umbrella sampling with hbond Giacomo Fiorin (Sat Mar 24 2012 - 12:52:17 CDT)
NAMD 2.9b1 crashes during minimization Francesco Pietra (Thu Mar 22 2012 - 10:28:04 CDT)
- AW: NAMD 2.9b1 crashes during minimization Norman Geist (Fri Mar 23 2012 - 01:58:15 CDT)
Glycosaminoglycan sulfate group with CHARMM Massimiliano Porrini (Thu Mar 22 2012 - 10:09:03 CDT)
- AW: Glycosaminoglycan sulfate group with CHARMM Norman Geist (Fri Mar 23 2012 - 01:48:05 CDT)
- Re: Glycosaminoglycan sulfate group with CHARMM Michelle Kuttel (Fri Mar 23 2012 - 02:20:29 CDT)
  - Re: Glycosaminoglycan sulfate group with CHARMM Massimiliano Porrini (Wed Mar 28 2012 - 12:18:08 CDT)
    - AW: Glycosaminoglycan sulfate group with CHARMM Norman Geist (Thu Mar 29 2012 - 00:58:54 CDT)
problem with paramters? Albert (Thu Mar 22 2012 - 00:25:27 CDT)
- AW: problem with paramters? Norman Geist (Thu Mar 22 2012 - 02:08:44 CDT)
conf file question Molecular Dynamics (Wed Mar 21 2012 - 04:19:57 CDT)
- AW: conf file question Norman Geist (Wed Mar 21 2012 - 10:27:19 CDT)
2.9b1 and GPU accelerated GB implicit solvent Aron Broom (Tue Mar 20 2012 - 23:16:57 CDT)
- Re: 2.9b1 and GPU accelerated GB implicit solvent David Tanner (Wed Mar 21 2012 - 12:41:23 CDT)
NAMD 2.9b1 released Jim Phillips (Tue Mar 20 2012 - 20:35:59 CDT)
will Jaguar enough for NAMD partial charge? Albert (Tue Mar 20 2012 - 02:18:54 CDT)
Collective variable on COM instead of COG poker_at_physics.usyd.edu.au (Mon Mar 19 2012 - 20:47:53 CDT)
- Re: Collective variable on COM instead of COG Jérôme Hénin (Tue Mar 20 2012 - 08:14:04 CDT)
Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Mon Mar 19 2012 - 18:31:40 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Norman Geist (Tue Mar 20 2012 - 01:36:34 CDT)
  - Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Tue Mar 20 2012 - 08:32:49 CDT)
DNA system and PH control raghav singh (Mon Mar 19 2012 - 12:42:31 CDT)
- Re: DNA system and PH control Aron Broom (Mon Mar 19 2012 - 12:54:11 CDT)
SMD under NPT ensemble raghav singh (Mon Mar 19 2012 - 10:12:17 CDT)
- Re: SMD under NPT ensemble Wang Yi (Mon Mar 19 2012 - 10:20:07 CDT)
  - Re: SMD under NPT ensemble johan strumpfer (Mon Mar 19 2012 - 11:28:25 CDT)
is it possible to strip the restrain linearly? Albert (Mon Mar 19 2012 - 08:29:00 CDT)
- Re: is it possible to strip the restrain linearly? Axel Kohlmeyer (Mon Mar 19 2012 - 08:37:10 CDT)
  - Re: is it possible to strip the restrain linearly? Albert (Mon Mar 19 2012 - 10:33:09 CDT)
    - Re: is it possible to strip the restrain linearly? Jérôme Hénin (Mon Mar 19 2012 - 11:33:16 CDT)
FEP tutorial-my molecule doesn't show up in VMD Alisha \ (Mon Mar 19 2012 - 01:20:44 CDT)
- Re: FEP tutorial-my molecule doesn't show up in VMD Chris Harrison (Mon Mar 19 2012 - 01:40:57 CDT)
  - Re: FEP tutorial-my molecule doesn't show up in VMD Alisha \ (Mon Mar 19 2012 - 01:56:38 CDT)
Tyrosine ligand at Fe(II) Francesco Pietra (Sun Mar 18 2012 - 11:34:57 CDT)
what does .inp do from CHARMM GUI? Albert (Sun Mar 18 2012 - 07:19:22 CDT)
- Re: what does .inp do from CHARMM GUI? Bjoern Olausson (Mon Mar 19 2012 - 07:42:46 CDT)
jobs failed Albert (Sat Mar 17 2012 - 14:33:19 CDT)
- Re: jobs failed Axel Kohlmeyer (Sat Mar 17 2012 - 14:52:17 CDT)
Simulations with alpha methylated amino acids amin_at_imtech.res.in (Fri Mar 16 2012 - 20:23:33 CDT)
NAMD on Bluegene Thomas Lemmin (Fri Mar 16 2012 - 12:39:16 CDT)
- Re: NAMD on Bluegene Axel Kohlmeyer (Sat Mar 17 2012 - 15:27:40 CDT)
ABF - coordNum collective variable Adam Skelton (Thu Mar 15 2012 - 15:27:07 CDT)
- Re: ABF - coordNum collective variable Giacomo Fiorin (Fri Mar 16 2012 - 10:59:38 CDT)
  - Re: ABF - coordNum collective variable Jérôme Hénin (Mon Mar 19 2012 - 10:47:45 CDT)
External electric field using Grid Mohammad Jomah Ibraheem Ali Abu Saude (mbusaude) (Thu Mar 15 2012 - 14:47:12 CDT)
selecting multiple fixed atom in SMD raghav singh (Thu Mar 15 2012 - 11:47:30 CDT)
Announcement: Large biomolecule benchmark report Hannes Loeffler (Thu Mar 15 2012 - 07:51:36 CDT)
restart a simulation upayan baul (Thu Mar 15 2012 - 07:20:42 CDT)
- Re: restart a simulation Aron Broom (Thu Mar 15 2012 - 09:19:20 CDT)
  - Re: restart a simulation upayan baul (Fri Mar 16 2012 - 06:51:28 CDT)
- AW: restart a simulation Norman Geist (Fri Mar 16 2012 - 02:01:34 CDT)
Apply two Different eFeild on the same Direction Mohammad Jomah Ibraheem Ali Abu Saude (mbusaude) (Thu Mar 15 2012 - 02:34:46 CDT)
center of mass movement removal throughout simulation? Markus K. Dahlgren (Mon Mar 12 2012 - 18:53:53 CDT)
- AW: center of mass movement removal throughout simulation? Norman Geist (Tue Mar 13 2012 - 01:32:45 CDT)
- AW: center of mass movement removal throughout simulation? Norman Geist (Tue Mar 13 2012 - 01:36:16 CDT)
  - Re: AW: center of mass movement removal throughout simulation? Markus K. Dahlgren (Tue Mar 13 2012 - 09:50:37 CDT)
    - Re: AW: center of mass movement removal throughout simulation? Aron Broom (Tue Mar 13 2012 - 11:30:38 CDT)
    - AW: AW: center of mass movement removal throughout simulation? Norman Geist (Wed Mar 14 2012 - 01:49:39 CDT)
Regarding Installing NAMD in Ubuntu amit majhi (Mon Mar 12 2012 - 11:44:48 CDT)
- Re: Regarding Installing NAMD in Ubuntu Axel Kohlmeyer (Mon Mar 12 2012 - 11:52:53 CDT)
Fw: forough askari (Sun Mar 11 2012 - 11:54:25 CDT)
Fwd: SOLVED, however multiple CUDA efficiency? Francesco Pietra (Sun Mar 11 2012 - 11:36:55 CDT)
CUDA error 0 attaching to node Francesco Pietra (Fri Mar 09 2012 - 09:12:19 CST)
- Fwd: CUDA error 0 attaching to node Francesco Pietra (Sat Mar 10 2012 - 00:32:08 CST)
  - Fwd: CUDA error 0 attaching to node Francesco Pietra (Sun Mar 11 2012 - 10:28:04 CDT)
is zeroMomentum safe in a steered MD simulation? Jose Borreguero (Fri Mar 09 2012 - 09:08:41 CST)
Compiling NAMD Marcel UJI (IMAP) (Fri Mar 09 2012 - 06:49:34 CST)
Missing angle parameters in the ffTK ¼¿ëÀÏ (Fri Mar 09 2012 - 01:38:08 CST)
- Re: Missing angle parameters in the ffTK Mayne, Christopher G (Fri Mar 09 2012 - 09:17:06 CST)
Compiling NAMD on NICS Kraken Alexander Predeus (Thu Mar 08 2012 - 22:39:05 CST)
- Re: Compiling NAMD on NICS Kraken Jernej Zidar (Thu Mar 08 2012 - 23:42:09 CST)
  - Re: Compiling NAMD on NICS Kraken Alexander Predeus (Fri Mar 09 2012 - 11:45:11 CST)
TclForces clearconfig cancels addforce calls? Niklaus Johner (Thu Mar 08 2012 - 15:32:39 CST)
Metadynamics Problems Aron Broom (Wed Mar 07 2012 - 17:13:23 CST)
- Re: Metadynamics Problems Axel Kohlmeyer (Wed Mar 07 2012 - 17:22:46 CST)
  - Re: Metadynamics Problems Aron Broom (Wed Mar 07 2012 - 17:29:38 CST)
geometry deformation lecan (Wed Mar 07 2012 - 15:10:27 CST)
- Re: geometry deformation Grace Brannigan (Wed Mar 07 2012 - 15:45:36 CST)
charmm param ... wrong charges raghav singh (Wed Mar 07 2012 - 08:44:50 CST)
- Re: charmm param ... wrong charges Cristhian Boetsch (Thu Mar 08 2012 - 12:49:35 CST)
  - Re: charmm param ... wrong charges Aron Broom (Thu Mar 08 2012 - 13:27:49 CST)
    - Re: charmm param ... wrong charges Raghav (Thu Mar 08 2012 - 17:31:24 CST)
    - Re: charmm param ... wrong charges Aron Broom (Thu Mar 08 2012 - 18:58:01 CST)
How to set protonation states of certain atom in DNA with namd/vmd raghav singh (Wed Mar 07 2012 - 07:15:55 CST)
how to calculate the box size mjyang (Tue Mar 06 2012 - 01:48:45 CST)
- Re: how to calculate the box size Aron Broom (Tue Mar 06 2012 - 08:44:57 CST)
  - Re: how to calculate the box size Axel Kohlmeyer (Tue Mar 06 2012 - 08:52:59 CST)
- Re: how to calculate the box size Cristhian Boetsch (Tue Mar 06 2012 - 10:48:30 CST)
  - AW: how to calculate the box size Norman Geist (Wed Mar 07 2012 - 01:01:31 CST)
    - RE: how to calculate the box size mjyang (Wed Mar 07 2012 - 01:27:17 CST)
Replica exchange and multiple time-stepping Niklaus Johner (Mon Mar 05 2012 - 10:19:10 CST)
Constant Pull Velocity ishiikai08_at_yahoo.co.jp (Mon Mar 05 2012 - 09:11:28 CST)
- Re: Constant Pull Velocity Wang Yi (Mon Mar 05 2012 - 09:59:28 CST)
  - Re:Re: Constant Pull Velocity ishiikai08_at_yahoo.co.jp (Mon Mar 05 2012 - 21:39:29 CST)
SMD-DNA : ABNORMAL EOF FOUND - buffer=*END* raghav singh (Mon Mar 05 2012 - 08:12:33 CST)
- Re: SMD-DNA : ABNORMAL EOF FOUND - buffer=*END* Aron Broom (Mon Mar 05 2012 - 08:31:31 CST)
- Re: SMD-DNA : ABNORMAL EOF FOUND - buffer=*END* Chris Harrison (Mon Mar 05 2012 - 09:11:54 CST)
system splitted lecan (Fri Mar 02 2012 - 06:54:50 CST)
- Re: system splitted Aron Broom (Fri Mar 02 2012 - 09:21:12 CST)
  - AW: system splitted Norman Geist (Mon Mar 05 2012 - 00:59:23 CST)
Internal Unit system Niklaus Johner (Thu Mar 01 2012 - 11:21:53 CST)
- Re: Internal Unit system Ajasja LjubetiÄ (Thu Mar 01 2012 - 12:14:21 CST)
  - Re: Internal Unit system Niklaus Johner (Thu Mar 01 2012 - 14:52:24 CST)
    - Re: Internal Unit system Victor Ovchinnikov (Thu Mar 01 2012 - 15:16:00 CST)
SHAKE Tolerance and Performance Aron Broom (Thu Mar 01 2012 - 01:04:28 CST)
- Re: SHAKE Tolerance and Performance Nicholas M Glykos (Thu Mar 01 2012 - 03:16:05 CST)
Protein ligand simulation Tutorial sai nitin (Wed Feb 29 2012 - 06:47:38 CST)
- Re: Protein ligand simulation Tutorial Chris Chipot (Wed Feb 29 2012 - 08:07:08 CST)
- Re: Protein ligand simulation Tutorial poker_at_physics.usyd.edu.au (Wed Feb 29 2012 - 17:01:06 CST)
drude water simulation bug ? radial distrubuion function Sergey (Wed Feb 29 2012 - 01:22:30 CST)
problem with installing NAMD in Linux Red Hat rukman kesh (Wed Feb 29 2012 - 00:40:12 CST)
- Re: problem with installing NAMD in Linux Red Hat Chris Harrison (Thu Mar 01 2012 - 00:17:28 CST)
  - Re: problem with installing NAMD in Linux Red Hat rukman kesh (Mon Mar 05 2012 - 01:39:38 CST)
rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens Aron Broom (Tue Feb 28 2012 - 21:58:25 CST)
- Re: rigidBonds water and langevinHydrogen off (no problem!) JC Gumbart (Thu Mar 01 2012 - 12:49:09 CST)
  - Re: rigidBonds water and langevinHydrogen off (no problem!) Aron Broom (Thu Mar 01 2012 - 13:27:59 CST)
- Re: rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens Jim Phillips (Thu Mar 01 2012 - 14:47:48 CST)
  - Re: rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens Aron Broom (Thu Mar 01 2012 - 15:06:29 CST)
    - Re: rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens Aron Broom (Fri Mar 02 2012 - 10:51:16 CST)
drude water simulation bug ? Sergey (Tue Feb 28 2012 - 14:35:26 CST)
Drug design issue. Boyang Wang (Tue Feb 28 2012 - 02:08:07 CST)
- Re: Drug design issue. Branko (Tue Feb 28 2012 - 05:39:26 CST)
R: restart file Chiara.cosenza (Sat Feb 25 2012 - 09:16:29 CST)
- Re: R: restart file Nicholas M Glykos (Sat Feb 25 2012 - 09:38:27 CST)
  - Re: R: restart file Aron Broom (Sat Feb 25 2012 - 11:00:24 CST)
restart file Namd Namd (Sat Feb 25 2012 - 07:31:18 CST)
- Re: restart file Aron Broom (Sat Feb 25 2012 - 08:43:56 CST)
Re: Consistent temperature increase in CUDA runs Aron Broom (Fri Feb 24 2012 - 14:49:28 CST)
- Re: Consistent temperature increase in CUDA runs Aron Broom (Fri Feb 24 2012 - 19:53:08 CST)
  - AW: Consistent temperature increase in CUDA runs Norman Geist (Mon Feb 27 2012 - 00:28:03 CST)
    - Re: AW: Consistent temperature increase in CUDA runs Axel Kohlmeyer (Tue Feb 28 2012 - 06:14:18 CST)
    - Re: AW: Consistent temperature increase in CUDA runs Nicholas M Glykos (Tue Feb 28 2012 - 08:40:29 CST)
- Re: Consistent temperature increase in CUDA runs Aron Broom (Mon Feb 27 2012 - 08:31:46 CST)
  - AW: Consistent temperature increase in CUDA runs Norman Geist (Tue Feb 28 2012 - 00:19:29 CST)
regarding ion concentration in implicit solvent Prathit Chatterjee (Fri Feb 24 2012 - 05:19:51 CST)
- Re: regarding ion concentration in implicit solvent Prathit Chatterjee (Wed Feb 29 2012 - 08:04:08 CST)
  - Re: regarding ion concentration in implicit solvent Nicholas M Glykos (Wed Feb 29 2012 - 08:29:40 CST)
  - Re: regarding ion concentration in implicit solvent Aron Broom (Wed Feb 29 2012 - 08:31:53 CST)
Consistent temperature increase in CUDA runs Norman Geist (Fri Feb 24 2012 - 00:51:38 CST)
what restraint can I use to prevent membrane diffusion on the Z-axis? Jose Borreguero (Wed Feb 22 2012 - 14:07:30 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? Chris Harrison (Sat Feb 25 2012 - 11:59:43 CST)
  - Re: what restraint can I use to prevent membrane diffusion on the Z-axis? kanchi subbarao rao (Sun Feb 26 2012 - 10:39:42 CST)
  - Re: what restraint can I use to prevent membrane diffusion on the Z-axis? kanchi subbarao rao (Tue Feb 28 2012 - 11:58:49 CST)
Error in NAMD 2.8 function Sereda, Yuriy Vladimirovich (Wed Feb 22 2012 - 11:02:09 CST)
- Re: Error in NAMD 2.8 function Chris Harrison (Thu Mar 01 2012 - 00:25:22 CST)
Re: Keep PBC box size in Z-direction constant? Bjoern Olausson (Wed Feb 22 2012 - 03:36:42 CST)
- Release of the R.E.D.-III.5 tools FyD (Wed Feb 22 2012 - 05:00:23 CST)
AW: Keep PBC box size in Z-direction constant? Norman Geist (Wed Feb 22 2012 - 00:24:02 CST)
Keep PBC box size in Z-direction constant? Bjoern Olausson (Mon Feb 20 2012 - 06:37:05 CST)
- AW: Keep PBC box size in Z-direction constant? Norman Geist (Tue Feb 21 2012 - 00:27:45 CST)
FW: vmd-l: Stand-alone VMD ? Mark Cunningham (Thu Feb 16 2012 - 15:45:55 CST)
Re: Possible bug or inconvenience Chris Harrison (Wed Feb 15 2012 - 15:12:03 CST)
RMSD metadynamics simone bardwell (Wed Feb 15 2012 - 13:25:16 CST)
- Re: RMSD metadynamics Giacomo Fiorin (Wed Feb 15 2012 - 13:48:50 CST)
  - Re: RMSD metadynamics simone bardwell (Wed Feb 15 2012 - 15:59:20 CST)
    - Re: RMSD metadynamics Giacomo Fiorin (Wed Feb 15 2012 - 16:38:03 CST)
    - Re: RMSD metadynamics Jérôme Hénin (Thu Feb 16 2012 - 02:39:04 CST)
how can i demonstrate that a chain-like molecule within a membrane. superdirac (Wed Feb 15 2012 - 07:19:36 CST)
- Re: how can i demonstrate that a chain-like molecule within a membrane. Chris Chipot (Wed Feb 15 2012 - 07:27:44 CST)
Possible bug or inconvenience Norman Geist (Wed Feb 15 2012 - 04:06:34 CST)
Graphene pdb/psf files cannot be read by psfgen Wanzhi Qiu (Wed Feb 15 2012 - 01:14:04 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Cruz-Chu Eduardo Roberto (Wed Feb 15 2012 - 05:06:31 CST)
  - Re: Graphene pdb/psf files cannot be read by psfgen kanchi subbarao rao (Wed Feb 15 2012 - 08:11:10 CST)
  - Re: Graphene pdb/psf files cannot be read by psfgen Wanzhi Qiu (Wed Feb 15 2012 - 20:06:01 CST)
martini force field Swarna M Patra (Tue Feb 14 2012 - 21:41:19 CST)
- Re: martini force field Chris Harrison (Wed Feb 15 2012 - 15:02:28 CST)
  - Re: martini force field Chris Harrison (Wed Feb 15 2012 - 15:09:45 CST)
Regarding thermostats felmerino_at_uchile.cl (Mon Feb 13 2012 - 09:21:33 CST)
- Re: Regarding thermostats Gianluca Interlandi (Mon Feb 13 2012 - 09:59:18 CST)
- Re: Regarding thermostats Marcos Sotomayor (Thu Feb 23 2012 - 16:37:03 CST)
where is psf develop in ffTK ¼¿ëÀÏ (Mon Feb 13 2012 - 06:55:37 CST)
- Re: where is psf develop in ffTK Chris Harrison (Wed Feb 15 2012 - 15:21:27 CST)
2CPU+1GPU vs 1CPU+2GPU Marcel UJI (IMAP) (Mon Feb 13 2012 - 05:21:18 CST)
- Re: 2CPU+1GPU vs 1CPU+2GPU Nicholas M Glykos (Mon Feb 13 2012 - 05:44:59 CST)
  - Re: 2CPU+1GPU vs 1CPU+2GPU Aron Broom (Mon Feb 13 2012 - 08:26:30 CST)
how to understand vdwForceSwitching Liqun Zhang (Sat Feb 11 2012 - 17:09:48 CST)
- Re: how to understand vdwForceSwitching Chris Harrison (Wed Feb 15 2012 - 15:50:33 CST)
parameter file for POPC (RBCG model) Swarna M Patra (Thu Feb 09 2012 - 22:29:21 CST)
RBCG-configuration file Swarna M Patra (Thu Feb 09 2012 - 05:53:15 CST)
Re: Copper ion moving out of the protein towards bulk solvent poker_at_physics.usyd.edu.au (Wed Feb 08 2012 - 18:24:50 CST)
How to calculate surface tension properly Bjoern Olausson (Wed Feb 08 2012 - 07:59:15 CST)
Copper ion moving out of the protein towards bulk solvent SUBHA KALYAANAMOORTHY (Tue Feb 07 2012 - 19:16:26 CST)
crossing the border by protein/ion complex Maria Bykhovskaia (Tue Feb 07 2012 - 17:16:30 CST)
- Re: crossing the border by protein/ion complex Axel Kohlmeyer (Tue Feb 07 2012 - 17:33:08 CST)
  - AW: crossing the border by protein/ion complex Norman Geist (Wed Feb 08 2012 - 00:54:30 CST)
Ewald contribution to pressure profile only working on single core Bjoern Olausson (Tue Feb 07 2012 - 06:59:43 CST)
Question about "Free Energy of Conformational Change Calculations" Shen, Han (Mon Feb 06 2012 - 11:03:44 CST)
- Re: Question about "Free Energy of Conformational Change Calculations" Giacomo Fiorin (Mon Feb 06 2012 - 11:13:21 CST)
gurukatagi@gmail.com Gurunath Katagi (Mon Feb 06 2012 - 10:37:49 CST)
- Re: gurukatagi@gmail.com Ajasja LjubetiÄ (Mon Feb 06 2012 - 11:05:26 CST)
  - Re: gurukatagi@gmail.com Aron Broom (Mon Feb 06 2012 - 12:09:08 CST)
  - Re: gurukatagi@gmail.com Gurunath Katagi (Wed Feb 22 2012 - 11:22:01 CST)
ffTK in the just released VMD 1.9.1 JC Gumbart (Sat Feb 04 2012 - 15:04:05 CST)
- AW: ffTK in the just released VMD 1.9.1 Norman Geist (Mon Feb 06 2012 - 01:04:05 CST)
  - RE: ffTK in the just released VMD 1.9.1 JC Gumbart (Mon Feb 06 2012 - 01:15:52 CST)
Hard sphere potential M.Raviprasad (Thu Feb 02 2012 - 20:20:14 CST)
- Re: Hard sphere potential Axel Kohlmeyer (Thu Feb 02 2012 - 20:56:09 CST)
  - RE: Hard sphere potential M.Raviprasad (Thu Feb 02 2012 - 22:18:23 CST)
    - Re: Hard sphere potential Axel Kohlmeyer (Thu Feb 02 2012 - 22:41:22 CST)
one question about gtp flipping in namd simulation Liqun Zhang (Thu Feb 02 2012 - 13:42:27 CST)
- Re: one question about gtp flipping in namd simulation Chris Harrison (Thu Feb 02 2012 - 13:49:56 CST)
RMSD collective variable - Different atons to align and to calculate RMSD Paulo Cesar Telles de Souza (Thu Feb 02 2012 - 12:19:10 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Giacomo Fiorin (Thu Feb 02 2012 - 13:52:49 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Chris Harrison (Thu Feb 02 2012 - 13:54:55 CST)
  - Re: RMSD collective variable - Different atons to align and to calculate RMSD Jérôme Hénin (Thu Feb 02 2012 - 15:40:47 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Davide Branduardi (Thu Feb 02 2012 - 14:27:18 CST)
NAMDenergy plugin_van der Waal interactions Bruno Luís Pinto de Oliveira (Thu Feb 02 2012 - 11:06:20 CST)
- Re: NAMDenergy plugin_van der Waal interactions Chris Harrison (Wed Feb 15 2012 - 15:27:12 CST)
  - RE: NAMDenergy plugin_van der Waal interactions Bruno Luís Pinto de Oliveira (Mon Feb 20 2012 - 07:01:14 CST)
Energy minimization of membrane R. Charbel Maroun (Thu Feb 02 2012 - 06:37:42 CST)
- Re: Energy minimization of membrane Boyang Wang (Thu Feb 02 2012 - 23:31:28 CST)
  - AW: Energy minimization of membrane Norman Geist (Fri Feb 03 2012 - 01:14:50 CST)
rigidBonds water option Hasan haska (Thu Feb 02 2012 - 01:48:22 CST)
- Re: rigidBonds water option Chris Harrison (Thu Feb 02 2012 - 14:02:37 CST)
Gromacs analysis tools for Namd output PAUL NEWMAN (Wed Feb 01 2012 - 11:41:40 CST)
- Re: vmd-l: Gromacs analysis tools for Namd output John Stone (Wed Feb 01 2012 - 11:47:43 CST)
- Re: Gromacs analysis tools for Namd output Axel Kohlmeyer (Wed Feb 01 2012 - 11:48:47 CST)
- RE: vmd-l: Gromacs analysis tools for Namd output Kei Sit (Wed Feb 01 2012 - 17:33:01 CST)
Analysis of FEP output file sudipta (Tue Jan 31 2012 - 11:41:33 CST)
- Re: Analysis of FEP output file Chris Harrison (Wed Feb 15 2012 - 15:29:59 CST)
  - Re: Analysis of FEP output file Chris Chipot (Thu Feb 16 2012 - 07:35:12 CST)
Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Tue Jan 31 2012 - 08:30:05 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Giacomo Fiorin (Tue Jan 31 2012 - 12:28:24 CST)
  - Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Wed Feb 01 2012 - 03:44:26 CST)
Fwd: Madhulika Gupta (Mon Jan 30 2012 - 22:10:37 CST)
problem to analyze the output of FEP file using vmd plugin sudipta (Mon Jan 30 2012 - 15:58:41 CST)
Installing NAMD on a 64-bit linux (NVIDIA CUDA) Shyno Mathew (Mon Jan 30 2012 - 12:15:15 CST)
- Re: Installing NAMD on a 64-bit linux (NVIDIA CUDA) Axel Kohlmeyer (Mon Jan 30 2012 - 12:24:40 CST)
  - AW: Installing NAMD on a 64-bit linux (NVIDIA CUDA) Norman Geist (Tue Jan 31 2012 - 00:53:47 CST)
Alchemical free-energy methods and electroneutrality Thomas Albers (Sat Jan 28 2012 - 13:35:27 CST)
- Re: Alchemical free-energy methods and electroneutrality Rajan Vatassery (Sat Jan 28 2012 - 15:31:18 CST)
- RE: Alchemical free-energy methods and electroneutrality JC Gumbart (Sat Jan 28 2012 - 15:47:54 CST)
Output of thermodynamic integration Kei-ichi Okazaki (Fri Jan 27 2012 - 18:16:47 CST)
- Re: Output of thermodynamic integration Jérôme Hénin (Sat Jan 28 2012 - 04:25:19 CST)
  - RE: Output of thermodynamic integration Okazaki, Keiichi (NIH/NIDDK) [F] (Sat Jan 28 2012 - 10:31:35 CST)
(no subject) Madhulika Gupta (Tue Jan 24 2012 - 23:08:52 CST)
- Re: Ajasja LjubetiÄ (Wed Jan 25 2012 - 12:05:49 CST)
  - Re: ÖÓË´ (Fri Jul 20 2012 - 02:38:00 CDT)
    - AW: Norman Geist (Fri Jul 20 2012 - 07:47:21 CDT)
  - Re: Jacqueline Schmidt (Wed Aug 29 2012 - 12:48:52 CDT)
NAMD on ranger.tacc Jesper Sørensen (Mon Jan 23 2012 - 10:28:33 CST)
- Re: NAMD on ranger.tacc George M Giambasu (Mon Jan 23 2012 - 11:26:26 CST)
  - Re: NAMD on ranger.tacc Jesper Sørensen (Tue Jan 24 2012 - 11:46:11 CST)
    - Re: NAMD on ranger.tacc George M Giambasu (Tue Jan 24 2012 - 12:22:42 CST)
    - Re: NAMD on ranger.tacc Jesper Sørensen (Tue Jan 24 2012 - 14:35:39 CST)
Umbrella sampling using dihedral angle Buddhadev Maiti (Sun Jan 22 2012 - 22:17:25 CST)
- Re: Umbrella sampling using dihedral angle Giacomo Fiorin (Tue Jan 24 2012 - 09:38:30 CST)
- Re: Umbrella sampling using dihedral angle Giacomo Fiorin (Tue Jan 24 2012 - 11:21:34 CST)
(no subject) Basak Isin (Mon Jan 23 2012 - 01:16:45 CST)
GBIS and hydrophobic solvation Gianluca Interlandi (Fri Jan 20 2012 - 18:41:27 CST)
- Re: GBIS and hydrophobic solvation David Tanner (Wed Feb 15 2012 - 15:36:31 CST)
  - Re: GBIS and hydrophobic solvation Gianluca Interlandi (Wed Feb 15 2012 - 15:45:54 CST)
Harmonic Constrain like MMFP in CHARMM Vahid Mirjalili (Fri Jan 20 2012 - 17:52:14 CST)
- Re: Harmonic Constrain like MMFP in CHARMM Giacomo Fiorin (Fri Jan 20 2012 - 18:42:26 CST)
  - Re: Harmonic Constrain like MMFP in CHARMM Vahid Mirjalili (Fri Jan 20 2012 - 19:41:28 CST)
    - Re: Harmonic Constrain like MMFP in CHARMM Giacomo Fiorin (Sat Jan 21 2012 - 01:24:14 CST)
    - Re: Harmonic Constrain like MMFP in CHARMM Vahid Mirjalili (Mon Jan 23 2012 - 14:56:55 CST)
  - Re: Harmonic Constrain like MMFP in CHARMM Giacomo Fiorin (Tue Jan 24 2012 - 09:40:08 CST)
Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue Gungor Ozer (Thu Jan 19 2012 - 11:44:29 CST)
- Re: Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue Giacomo Fiorin (Thu Jan 19 2012 - 11:56:00 CST)
- Re: Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue Boyang Wang (Thu Jan 19 2012 - 17:45:41 CST)
RE: spinAngle Giacomo Fiorin (Wed Jan 18 2012 - 13:06:47 CST)
Re: spinAngle Giacomo Fiorin (Wed Jan 18 2012 - 12:32:32 CST)
- Re: spinAngle Giacomo Fiorin (Wed Jan 18 2012 - 13:41:27 CST)
  - RE: spinAngle Buddhadev Maiti (Wed Jan 18 2012 - 16:28:58 CST)
    - Re: spinAngle Giacomo Fiorin (Wed Jan 18 2012 - 16:34:18 CST)
    - Re: Re: spinAngle Ajasja LjubetiÄ (Thu Jan 19 2012 - 05:13:15 CST)
namd question in parameter conversion Liqun Zhang (Wed Jan 18 2012 - 10:27:12 CST)
- Re: namd question in parameter conversion Aron Broom (Wed Jan 18 2012 - 12:35:01 CST)
- Re: namd question in parameter conversion Boyang Wang (Thu Jan 19 2012 - 02:08:46 CST)
questions regarding ABF sampling in a DMPC bilayer Ajasja LjubetiÄ (Wed Jan 18 2012 - 08:12:20 CST)
- Re: questions regarding ABF sampling in a DMPC bilayer Jérôme Hénin (Wed Jan 18 2012 - 12:00:28 CST)
  - Re: questions regarding ABF sampling in a DMPC bilayer felmerino_at_uchile.cl (Wed Jan 18 2012 - 12:27:31 CST)
    - Re: questions regarding ABF sampling in a DMPC bilayer Giacomo Fiorin (Wed Jan 18 2012 - 13:13:50 CST)
  - Re: questions regarding ABF sampling in a DMPC bilayer Ajasja LjubetiÄ (Fri Jan 27 2012 - 08:03:54 CST)
    - Re: questions regarding ABF sampling in a DMPC bilayer Jérôme Hénin (Fri Jan 27 2012 - 09:10:44 CST)
    - Re: questions regarding ABF sampling in a DMPC bilayer Ajasja LjubetiÄ (Mon Jan 30 2012 - 06:49:52 CST)
- Re: questions regarding ABF sampling in a DMPC bilayer Giacomo Fiorin (Wed Jan 18 2012 - 12:05:02 CST)
question about NPT oguz gurbulak (Wed Jan 18 2012 - 02:06:19 CST)
- RE: question about NPT JC Gumbart (Wed Jan 18 2012 - 12:36:43 CST)
- Re: question about NPT Boyang Wang (Thu Jan 19 2012 - 02:16:03 CST)
  - Re: question about NPT oguz gurbulak (Thu Jan 19 2012 - 03:51:42 CST)
    - Re: question about NPT Boyang Wang (Thu Jan 19 2012 - 04:03:21 CST)
  - Re: question about NPT Axel Kohlmeyer (Thu Jan 19 2012 - 05:14:04 CST)
target pressure value Namd Namd (Tue Jan 17 2012 - 06:30:20 CST)
- target pressure value Namd Namd (Tue Jan 17 2012 - 06:32:45 CST)
  - Re: target pressure value Ajasja LjubetiÄ (Tue Jan 17 2012 - 07:03:36 CST)
Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Mon Jan 16 2012 - 19:29:26 CST)
- Re: Controlling fans on a GTX 560 ti Ajasja LjubetiÄ (Tue Jan 17 2012 - 08:25:29 CST)
  - Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Tue Jan 17 2012 - 08:35:42 CST)
    - Re: Controlling fans on a GTX 560 ti Ajasja LjubetiÄ (Tue Jan 17 2012 - 09:10:51 CST)
Problems in setting up low pH systems Sheng, Zi-Zhang (Wed Jan 11 2012 - 09:43:31 CST)
- Re: Problems in setting up low pH systems Giacomo Fiorin (Wed Jan 11 2012 - 10:03:34 CST)
surfaceTensionTarget - Surface Tension per interface or per bilayer Jon Fuller (Wed Jan 11 2012 - 04:25:24 CST)
- Re: surfaceTensionTarget - Surface Tension per interface or per bilayer Boyang Wang (Wed Jan 11 2012 - 08:30:17 CST)
  - Re: surfaceTensionTarget - Surface Tension per interface or per bilayer Jérôme Hénin (Wed Jan 11 2012 - 09:18:39 CST)
how does namd handle violations of the minimum image convention? Ana Celia Vila Verde (Mon Jan 09 2012 - 05:32:32 CST)
- Re: how does namd handle violations of the minimum image convention? Boyang Wang (Tue Jan 10 2012 - 21:45:04 CST)
Re: incompatibility between NAMD and amber topology files Osman, Roman (Tue Jan 10 2012 - 15:33:43 CST)
ERROR: 0031-250 task 0: Terminated Gurunath Katagi (Mon Jan 09 2012 - 23:42:53 CST)
incompatibility between NAMD and amber topology files Osman, Roman (Mon Jan 09 2012 - 16:13:24 CST)
ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing Gurunath Katagi (Tue Jan 10 2012 - 14:03:03 CST)
- RE: ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing Bennion, Brian (Tue Jan 10 2012 - 14:18:06 CST)
- Re: ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing Axel Kohlmeyer (Tue Jan 10 2012 - 14:21:26 CST)
Problem with parameter file in Pair Interaction Calculation M Mahjour (Mon Jan 09 2012 - 05:47:20 CST)
- Re: Problem with parameter file in Pair Interaction Calculation Boyang Wang (Mon Jan 09 2012 - 08:27:02 CST)
  - AW: Problem with parameter file in Pair Interaction Calculation Norman Geist (Tue Jan 10 2012 - 00:41:23 CST)
    - Re: AW: Problem with parameter file in Pair Interaction Calculation Kovacs, Sandor (Tue Jan 10 2012 - 01:14:04 CST)
    - Re: AW: Problem with parameter file in Pair Interaction Calculation M Mahjour (Tue Jan 10 2012 - 10:48:33 CST)
can TMD alignment prior to force calculation be turned off? Michael Zimmermann (Sun Jan 08 2012 - 15:04:15 CST)
- Re: can TMD alignment prior to force calculation be turned off? Axel Kohlmeyer (Sun Jan 08 2012 - 15:19:55 CST)
  - Re: can TMD alignment prior to force calculation be turned off? Michael Zimmermann (Sun Jan 08 2012 - 17:03:41 CST)
    - Re: can TMD alignment prior to force calculation be turned off? Jérôme Hénin (Sun Jan 08 2012 - 17:18:28 CST)
Problem with parameter file in Pair Interaction Calculation M Mahjour (Sun Jan 08 2012 - 00:14:50 CST)
IB fabrics Thomas Bishop (Fri Jan 06 2012 - 11:42:53 CST)
- Re: IB fabrics Axel Kohlmeyer (Fri Jan 06 2012 - 11:58:14 CST)
  - RE: IB fabrics Bennion, Brian (Fri Jan 06 2012 - 12:39:04 CST)
ABF simulation Tugba Nogay (Fri Jan 06 2012 - 10:53:36 CST)
- Re: ABF simulation Jérôme Hénin (Sat Jan 07 2012 - 05:16:24 CST)
Problem running NAMD 2.8 with ibverbs Moritz Schlarb (Fri Jan 06 2012 - 09:29:18 CST)
- Re: Problem running NAMD 2.8 with ibverbs Moritz Schlarb (Fri Jan 06 2012 - 09:41:49 CST)
  - AW: Problem running NAMD 2.8 with ibverbs Norman Geist (Mon Jan 09 2012 - 00:32:06 CST)
    - Re: Problem running NAMD 2.8 with ibverbs Moritz Schlarb (Wed Jan 11 2012 - 04:20:57 CST)
    - AW: Problem running NAMD 2.8 with ibverbs Norman Geist (Thu Jan 12 2012 - 07:34:31 CST)
TIP5P simulation Mallajosyula, Sairam (Thu Jan 05 2012 - 21:41:05 CST)
- Re: TIP5P simulation Axel Kohlmeyer (Thu Jan 05 2012 - 21:59:12 CST)
  - RE: TIP5P simulation Mallajosyula, Sairam (Fri Jan 06 2012 - 09:58:54 CST)
Problem with NVE simulation gaborekt_at_duq.edu (Thu Jan 05 2012 - 15:42:10 CST)
- Re: Problem with NVE simulation Axel Kohlmeyer (Thu Jan 05 2012 - 16:48:47 CST)
TIP4P force field Udaysankar Midya (Tue Jan 03 2012 - 21:46:52 CST)
- Re: TIP4P force field Boyang Wang (Tue Jan 03 2012 - 22:33:07 CST)
Re: Replica Exchange Discrete Molecular Dynamics for structure based models bharat gupta (Tue Jan 03 2012 - 00:48:16 CST)
water molecules oguz gurbulak (Mon Jan 02 2012 - 06:04:08 CST)
- Re: water molecules Nicholas M Glykos (Mon Jan 02 2012 - 07:35:19 CST)
  - Re: water molecules Boyang Wang (Tue Jan 03 2012 - 02:51:56 CST)
    - Re: water molecules oguz gurbulak (Tue Jan 03 2012 - 03:08:58 CST)
- AW: water molecules Norman Geist (Tue Jan 03 2012 - 00:34:15 CST)
(no subject) ÐìÖÓºÓ (Mon Jan 02 2012 - 03:03:31 CST)
AW: scaling Norman Geist (Mon Jan 02 2012 - 00:44:13 CST)

Last message date: Tue Dec 31 2013 - 11:28:27 CST
Archived on: Tue Dec 31 2013 - 23:24:07 CST

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