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NAMD-L: By Thread

By Thread

3750 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive

Starting: Thu Jan 03 2013 - 06:24:44 CST
Ending: Tue Dec 30 2014 - 07:38:36 CST

angles between residues luca belmonte (Tue Dec 30 2014 - 07:38:14 CST)
Lone Pair on H2S JAVAD NOROOZI (Tue Dec 30 2014 - 06:05:39 CST)
Lone Pair on H2S JAVAD NOROOZI (Tue Dec 30 2014 - 06:05:40 CST)
Lone Pair on H2S JAVAD NOROOZI (Sat Dec 27 2014 - 09:42:25 CST)
warnings while using amber files amin_at_imtech.res.in (Thu Dec 25 2014 - 05:14:20 CST)
- Re: warnings while using amber files amin_at_imtech.res.in (Thu Dec 25 2014 - 21:54:38 CST)
NAMD 2.10b1: occasional corrupted frame in binary dcd output Tristan Croll (Tue Dec 23 2014 - 16:39:46 CST)
Cannot find colvar dih1 (dih colvars) Francesco Pietra (Tue Dec 23 2014 - 11:15:31 CST)
- Fwd: Cannot find colvar dih1 (dih colvars) Francesco Pietra (Tue Dec 23 2014 - 14:23:04 CST)
  - Fwd: Cannot find colvar dih1 (dih colvars) Francesco Pietra (Tue Dec 23 2014 - 15:01:39 CST)
Error on write to binary file Mihaela Drenscko (Mon Dec 22 2014 - 18:02:54 CST)
- AW: Error on write to binary file Norman Geist (Tue Dec 23 2014 - 02:42:04 CST)
.inpcrd to .pdb Shalton Evans (Sun Dec 21 2014 - 13:56:30 CST)
- Re: .inpcrd to .pdb Jason Swails (Sun Dec 21 2014 - 20:04:39 CST)
Free Energy Workshop, Münster, March 9-11Q_2015?= Vlad Cojocaru (Fri Dec 19 2014 - 12:02:00 CST)
Re: FATAL ERROR: seek failed while writing DCD file: No such file or directory Douglas Houston (Fri Dec 19 2014 - 08:33:31 CST)
problem in installation of charm-6.4.0 in bluegeneL] Santosh Kumar Chaudhary (Fri Dec 19 2014 - 05:49:45 CST)
FATAL ERROR: seek failed while writing DCD file: No such file or directory Douglas Houston (Thu Dec 18 2014 - 14:39:51 CST)
- AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory Norman Geist (Fri Dec 19 2014 - 00:35:26 CST)
  - Re: AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory Douglas Houston (Fri Dec 19 2014 - 02:12:48 CST)
    - Re: AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory Maxime Boissonneault (Fri Dec 19 2014 - 08:18:38 CST)
    - Re: AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory Douglas Houston (Fri Dec 19 2014 - 08:40:04 CST)
Re: Asking help on results of our GPU benchmark å‘¨æ–‡æ˜Œ (Thu Dec 18 2014 - 13:24:59 CST)
- AW: Asking help on results of our GPU benchmark Norman Geist (Fri Dec 19 2014 - 00:30:22 CST)
- Re: Asking help on results of our GPU benchmark å‘¨æ–‡æ˜Œ (Fri Dec 19 2014 - 16:06:33 CST)
  - AW: Asking help on results of our GPU benchmark Norman Geist (Mon Dec 22 2014 - 01:16:12 CST)
- Re: Asking help on results of our GPU benchmark å‘¨æ–‡æ˜Œ (Mon Dec 22 2014 - 12:11:18 CST)
  - AW: Asking help on results of our GPU benchmark Norman Geist (Tue Dec 23 2014 - 02:34:58 CST)
- Re: Asking help on results of our GPU benchmark å‘¨æ–‡æ˜Œ (Tue Dec 23 2014 - 14:05:30 CST)
Re: Constant Pressure, Variable Volume, Minimization Miss. State (Thu Dec 18 2014 - 13:01:05 CST)
- Re: Re: Constant Pressure, Variable Volume, Minimization Josh Vermaas (Thu Dec 18 2014 - 13:17:35 CST)
Asking help on results of our GPU benchmark å‘¨æ–‡æ˜Œ (Wed Dec 17 2014 - 15:13:24 CST)
- AW: Asking help on results of our GPU benchmark Norman Geist (Thu Dec 18 2014 - 02:39:51 CST)
Loading Velocity DCD file JAVAD NOROOZI (Wed Dec 17 2014 - 13:23:20 CST)
- AW: Loading Velocity DCD file Norman Geist (Thu Dec 18 2014 - 02:31:16 CST)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Dec 17 2014 - 10:24:50 CST)
setting up namd simulation in IBM Blue Gene/L Santosh Kumar Chaudhary (Wed Dec 17 2014 - 06:21:17 CST)
- RE: setting up namd simulation in IBM Blue Gene/L hannes.loeffler_at_stfc.ac.uk (Wed Dec 17 2014 - 07:07:23 CST)
  - RE: setting up namd simulation in IBM Blue Gene/L Santosh Kumar Chaudhary (Thu Dec 18 2014 - 00:09:48 CST)
    - RE: setting up namd simulation in IBM Blue Gene/L hannes.loeffler_at_stfc.ac.uk (Thu Dec 18 2014 - 01:36:36 CST)
    - RE: setting up namd simulation in IBM Blue Gene/L hannes.loeffler_at_stfc.ac.uk (Thu Dec 18 2014 - 01:43:11 CST)
- Re: setting up namd simulation in IBM Blue Gene/L Jim Phillips (Fri Dec 19 2014 - 12:55:33 CST)
  - Re: setting up namd simulation in IBM Blue Gene/L Santosh Kumar Chaudhary (Sat Dec 20 2014 - 01:53:14 CST)
Implementing the Virtual Bond Algorithm Using Colvars David Huggins (Wed Dec 17 2014 - 06:25:33 CST)
- Re: Implementing the Virtual Bond Algorithm Using Colvars Giacomo Fiorin (Thu Dec 18 2014 - 19:37:06 CST)
Extracting Kinetic Energy of Certain Atoms JAVAD NOROOZI (Wed Dec 17 2014 - 03:19:09 CST)
Is it so different when setting reinitvels or not? Zhao Lina (Wed Dec 17 2014 - 00:03:25 CST)
- Re: Is it so different when setting reinitvels or not? Jeff Comer (Wed Dec 17 2014 - 05:45:09 CST)
  - Re: Is it so different when setting reinitvels or not? Zhao Lina (Wed Dec 17 2014 - 19:31:49 CST)
Transferring bond list to new molecule Mert GÃ¼r (Tue Dec 16 2014 - 23:17:02 CST)
- Re: Transferring bond list to new molecule Josh Vermaas (Wed Dec 17 2014 - 08:18:18 CST)
  - Re: Transferring bond list to new molecule Mert GÃ¼r (Wed Dec 17 2014 - 18:06:05 CST)
Running Charmrun/NAMD with more than 10 processes fails K Miura (Tue Dec 16 2014 - 02:53:36 CST)
- AW: Running Charmrun/NAMD with more than 10 processes fails Norman Geist (Tue Dec 16 2014 - 04:06:49 CST)
Inspiration for most efficient implementation of coarse grained forcefield. Ajasja LjubetiÄ (Mon Dec 15 2014 - 12:08:03 CST)
- Re: Inspiration for most efficient implementation of coarse grained forcefield. JÃ©rÃ´me HÃ©nin (Mon Dec 15 2014 - 15:41:22 CST)
- Re: Inspiration for most efficient implementation of coarse grained forcefield. Jim Phillips (Tue Dec 16 2014 - 09:30:40 CST)
Error compiling NAMD2.9 after patching with PLUMED2.1 RubÃ©n Granero (Mon Dec 15 2014 - 06:47:27 CST)
- Re: Error compiling NAMD2.9 after patching with PLUMED2.1 Jim Phillips (Mon Dec 15 2014 - 08:37:26 CST)
  - Re: Error compiling NAMD2.9 after patching with PLUMED2.1 RubÃ©n Granero (Tue Dec 16 2014 - 07:39:02 CST)
    - Re: Error compiling NAMD2.9 after patching with PLUMED2.1 Jim Phillips (Tue Dec 16 2014 - 09:22:04 CST)
    - Re: Error compiling NAMD2.9 after patching with PLUMED2.1 RubÃ©n Granero (Tue Dec 16 2014 - 12:07:45 CST)
NAMD 2.10 released Jim Phillips (Fri Dec 12 2014 - 16:35:38 CST)
Info: Pairlistdist is too small for 3 computes during timestep 115001 Santosh Kumar Chaudhary (Fri Dec 12 2014 - 10:34:41 CST)
- Re: Info: Pairlistdist is too small for 3 computes during timestep 115001 Jim Phillips (Fri Dec 12 2014 - 15:49:06 CST)
- Re: Info: Pairlistdist is too small for 3 computes during timestep 115001 Subbarao Kanchi (Fri Dec 12 2014 - 16:26:26 CST)
question about FEP for amphiphile in lipid bilayer Leonardo Darre (Wed Dec 10 2014 - 08:08:27 CST)
- Re: question about FEP for amphiphile in lipid bilayer Giacomo Fiorin (Wed Dec 10 2014 - 08:41:25 CST)
  - Re: question about FEP for amphiphile in lipid bilayer Leonardo Darre (Wed Dec 10 2014 - 09:20:51 CST)
the difference of PCA and EDA ÂÀÐ¡Ó¨ (Wed Dec 10 2014 - 02:31:30 CST)
- Re: the difference of PCA and EDA Fotis Baltoumas (Wed Dec 10 2014 - 05:36:43 CST)
  - Re: the difference of PCA and EDA Hannes Loeffler (Wed Dec 10 2014 - 05:59:37 CST)
Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014 FyD (Tue Dec 09 2014 - 02:43:22 CST)
Choosing of windows and width for Umbrella Sampling Kevin C Chan (Mon Dec 08 2014 - 06:48:19 CST)
- Re: Choosing of windows and width for Umbrella Sampling Giacomo Fiorin (Mon Dec 08 2014 - 08:29:49 CST)
  - Re: Choosing of windows and width for Umbrella Sampling Kevin C Chan (Mon Dec 08 2014 - 09:39:46 CST)
query about the cross term in psf Kshatresh Dutta Dubey (Sat Dec 06 2014 - 13:31:42 CST)
- Re: query about the cross term in psf Josh Vermaas (Sat Dec 06 2014 - 13:49:06 CST)
  - Re: query about the cross term in psf Kshatresh Dutta Dubey (Sat Dec 06 2014 - 14:12:31 CST)
    - Re: query about the cross term in psf Josh Vermaas (Sat Dec 06 2014 - 14:22:32 CST)
colvars angle centerReference Jeff Comer (Fri Dec 05 2014 - 15:00:44 CST)
- Re: colvars angle centerReference Giacomo Fiorin (Tue Dec 09 2014 - 18:35:22 CST)
  - Re: colvars angle centerReference Jeff Comer (Tue Dec 09 2014 - 21:41:26 CST)
information about simulation speed Kshatresh Dutta Dubey (Tue Dec 02 2014 - 16:50:11 CST)
- Re: information about simulation speed Axel Kohlmeyer (Tue Dec 02 2014 - 16:53:44 CST)
  - Re: information about simulation speed Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:04:31 CST)
Running CUDA-enabled NAMD on multiple nodes without InfiniBand? Michel van der List (Mon Dec 01 2014 - 08:40:46 CST)
- AW: Running CUDA-enabled NAMD on multiple nodes without InfiniBand? Norman Geist (Mon Dec 01 2014 - 09:19:24 CST)
  - RE: Running CUDA-enabled NAMD on multiple nodes without InfiniBand? Michel van der List (Wed Dec 03 2014 - 12:06:03 CST)
    - AW: Running CUDA-enabled NAMD on multiple nodes without InfiniBand? Norman Geist (Thu Dec 04 2014 - 01:08:09 CST)
question about CUDA-enabled maryam atabay (Sat Nov 29 2014 - 10:19:49 CST)
- Re: question about CUDA-enabled Abhishek Tyagi (Sat Nov 29 2014 - 11:04:55 CST)
  - Re: question about CUDA-enabled Abhishek TYAGI (Sun Nov 30 2014 - 02:57:53 CST)
    - AW: question about CUDA-enabled Norman Geist (Mon Dec 01 2014 - 02:05:20 CST)
    - AW: question about CUDA-enabled Norman Geist (Mon Dec 01 2014 - 02:56:08 CST)
- Re: question about CUDA-enabled Axel Kohlmeyer (Sat Nov 29 2014 - 19:22:55 CST)
running NAMD in parallel Kshatresh Dutta Dubey (Fri Nov 28 2014 - 19:29:43 CST)
- Re: running NAMD in parallel Jim Phillips (Sat Nov 29 2014 - 16:51:06 CST)
Re: anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 04:04:49 CST)
- AW: anisotropic pressure control Norman Geist (Wed Nov 26 2014 - 05:04:20 CST)
  - Re: anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 05:10:09 CST)
Fw: anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 03:47:41 CST)
anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 02:48:51 CST)
- AW: anisotropic pressure control Norman Geist (Wed Nov 26 2014 - 03:22:31 CST)
colvar DistanceZ Kevin C Chan (Tue Nov 25 2014 - 21:03:55 CST)
- Re: colvar DistanceZ JÃ©rÃ´me HÃ©nin (Wed Nov 26 2014 - 05:07:19 CST)
  - Re: colvar DistanceZ Kevin C Chan (Wed Nov 26 2014 - 07:25:03 CST)
    - Re: colvar DistanceZ JÃ©rÃ´me HÃ©nin (Wed Nov 26 2014 - 07:35:37 CST)
    - Re: colvar DistanceZ Kevin C Chan (Wed Nov 26 2014 - 20:32:24 CST)
(no subject) flavio seixas (Tue Nov 25 2014 - 19:13:24 CST)
- AW: Norman Geist (Wed Nov 26 2014 - 02:26:35 CST)
  - Re: AW: flavio seixas (Wed Nov 26 2014 - 09:53:23 CST)
- (no subject) tillmann.utesch_at_mailbox.tu-berlin.de (Wed Nov 26 2014 - 03:20:51 CST)
question about CUDA-enabled maryam atabay (Tue Nov 25 2014 - 01:05:32 CST)
Colvars error Kevin C Chan (Tue Nov 25 2014 - 00:10:05 CST)
- Re: Colvars error Kevin C Chan (Tue Nov 25 2014 - 00:57:45 CST)
- Re: Colvars error Subbarao Kanchi (Tue Nov 25 2014 - 02:08:45 CST)
  - Re: Colvars error Kevin C Chan (Tue Nov 25 2014 - 05:11:55 CST)
    - Re: Colvars error Subbarao Kanchi (Tue Nov 25 2014 - 06:30:36 CST)
- Re: Colvars error Giacomo Fiorin (Tue Nov 25 2014 - 08:53:58 CST)
  - Re: Colvars error Kevin C Chan (Tue Nov 25 2014 - 21:11:41 CST)
"BAK" format files Ramin Ekhteiari (Mon Nov 24 2014 - 06:52:20 CST)
Fwd: question about CUDA-enabled maryam atabay (Mon Nov 24 2014 - 05:08:04 CST)
CGenFF atom type N- Francesco Pietra (Mon Nov 24 2014 - 02:55:04 CST)
Misleading failure of VMD with charge/CGenFF from waterbox Francesco Pietra (Sun Nov 23 2014 - 03:21:38 CST)
Fwd: Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files Francesco Pietra (Sat Nov 22 2014 - 02:45:10 CST)
11/22/2014 6:32:52 PM jeremy adler (Sat Nov 22 2014 - 00:32:52 CST)
A problem in ABF simulations Azadeh Alavi (Sat Nov 22 2014 - 05:50:03 CST)
- Re: A problem in ABF simulations Jeff Comer (Mon Nov 24 2014 - 11:44:45 CST)
tilt colvar JC Gumbart (Fri Nov 21 2014 - 11:09:55 CST)
- Re: tilt colvar Giacomo Fiorin (Fri Nov 21 2014 - 11:35:25 CST)
  - Re: tilt colvar JC Gumbart (Fri Nov 21 2014 - 18:12:31 CST)
  - Re: tilt colvar JC Gumbart (Tue Dec 02 2014 - 18:30:22 CST)
problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 09:09:52 CST)
- Re: problems with in text mode towards pdf and pdb files Jim Phillips (Fri Nov 21 2014 - 09:29:35 CST)
  - Re: problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 09:39:56 CST)
create psf file without hydrogens Revthi Sanker (Thu Nov 20 2014 - 12:26:48 CST)
- Re: create psf file without hydrogens Tristan Croll (Thu Nov 20 2014 - 14:22:06 CST)
  - Re: create psf file without hydrogens Revthi Sanker (Fri Nov 21 2014 - 03:23:19 CST)
carboxyl NBFIX on proteins Jeff Comer (Thu Nov 20 2014 - 09:18:45 CST)
- Re: carboxyl NBFIX on proteins Giacomo Fiorin (Thu Nov 20 2014 - 10:05:10 CST)
  - Re: carboxyl NBFIX on proteins Jeff Comer (Thu Nov 20 2014 - 10:46:35 CST)
about the vdw Interpolation calculation in NAMD source code Â¬Óíï¿ (Thu Nov 20 2014 - 02:44:40 CST)
- Re: about the vdw Interpolation calculation in NAMD source code Jeff Comer (Thu Nov 20 2014 - 08:20:54 CST)
- Re: about the vdw Interpolation calculation in NAMD source code Jim Phillips (Thu Nov 20 2014 - 08:29:27 CST)
  - Re: Re: about the vdw Interpolation calculation in NAMD source code Â¬Óíï¿ (Thu Nov 20 2014 - 09:32:10 CST)
    - Re: Re: about the vdw Interpolation calculation in NAMD source code Jim Phillips (Thu Nov 20 2014 - 16:00:29 CST)
    - Re: Re: Re: about the vdw Interpolation calculation in NAMD source code Â¬Óíï¿ (Thu Nov 20 2014 - 20:35:48 CST)
Topology and parameter files for some engineered residues KK R (Wed Nov 19 2014 - 09:31:33 CST)
Re: About NAMD Douglas Houston (Tue Nov 18 2014 - 09:32:59 CST)
- AW: About NAMD Norman Geist (Wed Nov 19 2014 - 01:10:11 CST)
  - Re: AW: About NAMD Douglas Houston (Wed Nov 26 2014 - 05:28:39 CST)
NAMD 2.10b2 released Jim Phillips (Mon Nov 17 2014 - 14:22:52 CST)
Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Mon Nov 17 2014 - 07:41:31 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Giacomo Fiorin (Mon Nov 17 2014 - 08:49:18 CST)
  - Re: Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Mon Nov 17 2014 - 09:57:37 CST)
how to fix the problem Liqun Zhang (Fri Nov 14 2014 - 17:19:37 CST)
- Re: how to fix the problem Jeff Comer (Fri Nov 14 2014 - 20:02:09 CST)
  - Re: how to fix the problem Jeff Comer (Fri Nov 14 2014 - 20:02:44 CST)
  - Re: how to fix the problem Jeff Comer (Sat Nov 15 2014 - 08:33:54 CST)
water-protein interation sunyeping (Fri Nov 14 2014 - 02:32:11 CST)
- RE: water-protein interation Hongbo Du (Fri Nov 14 2014 - 09:03:37 CST)
Atomselect for coor, vel, xsc Kevin C Chan (Thu Nov 13 2014 - 22:49:02 CST)
- Re: Atomselect for coor, vel, xsc Josh Vermaas (Fri Nov 14 2014 - 08:58:29 CST)
  - Re: Atomselect for coor, vel, xsc Axel Kohlmeyer (Fri Nov 14 2014 - 09:02:47 CST)
    - Re: Atomselect for coor, vel, xsc Kevin C Chan (Fri Nov 21 2014 - 04:20:16 CST)
Umbrella Sampling in NAMD Kevin C Chan (Thu Nov 13 2014 - 10:25:13 CST)
Simulation of a membrane protein with large extracellular domains Fotis Baltoumas (Thu Nov 13 2014 - 07:30:54 CST)
- Re: Simulation of a membrane protein with large extracellular domains Josh Vermaas (Thu Nov 13 2014 - 08:35:43 CST)
- Re: Simulation of a membrane protein with large extracellular domains Jim Phillips (Thu Nov 13 2014 - 16:05:08 CST)
APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) Bin He (Thu Nov 13 2014 - 01:53:42 CST)
- Re: APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) Jim Phillips (Thu Nov 13 2014 - 15:47:52 CST)
namd simulation for solids withoy solvation Subbusinger N (Thu Nov 13 2014 - 00:02:42 CST)
- Re: namd simulation for solids withoy solvation Kenno Vanommeslaeghe (Thu Nov 13 2014 - 11:50:51 CST)
  - Re: namd simulation for solids withoy solvation Subbusinger N (Fri Nov 14 2014 - 00:20:24 CST)
unsubscribe Gurpreet Kaur Dhindsa (Wed Nov 12 2014 - 19:04:28 CST)
Can NAMD does Langevin Dynamics Simulation Fidan Sumbul (Wed Nov 12 2014 - 14:48:25 CST)
- Re: Can NAMD does Langevin Dynamics Simulation Jeff Comer (Wed Nov 12 2014 - 16:37:31 CST)
  - Re: Can NAMD does Langevin Dynamics Simulation Fidan Sumbul (Thu Nov 13 2014 - 10:41:39 CST)
    - Re: Can NAMD does Langevin Dynamics Simulation Jeff Comer (Thu Nov 13 2014 - 14:37:13 CST)
    - Re: Can NAMD does Langevin Dynamics Simulation Jeff Comer (Thu Nov 13 2014 - 15:11:10 CST)
SOD topology with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 11:02:22 CST)
- Re: SOD topology with CHARMM36 Josh Vermaas (Tue Nov 11 2014 - 11:08:26 CST)
  - Re: SOD topology with CHARMM36 Kenno Vanommeslaeghe (Tue Nov 11 2014 - 12:27:08 CST)
Dioxygen atom type with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 10:11:00 CST)
- Re: Dioxygen atom type with CHARMM36 Kenno Vanommeslaeghe (Tue Nov 11 2014 - 11:07:25 CST)
  - Re: Dioxygen atom type with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 11:19:17 CST)
Re: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Bin He (Mon Nov 10 2014 - 13:51:15 CST)
- AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Norman Geist (Tue Nov 11 2014 - 02:48:52 CST)
- Re: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Bin He (Tue Nov 11 2014 - 06:19:06 CST)
  - AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Norman Geist (Tue Nov 11 2014 - 07:03:53 CST)
AW: FATAL ERROR: error parsing config file while executing <feff> Norman Geist (Mon Nov 10 2014 - 08:20:48 CST)
- Re: AW: FATAL ERROR: error parsing config file while executing <feff> Jim Phillips (Mon Nov 10 2014 - 15:44:39 CST)
Reg: QM/MM calculations in NAMD Akshay Bhatnagar (Mon Nov 10 2014 - 07:05:40 CST)
- AW: Reg: QM/MM calculations in NAMD Norman Geist (Mon Nov 10 2014 - 08:12:44 CST)
FATAL ERROR: error parsing config file while executing <feff> Mihaela Drenscko (Sun Nov 09 2014 - 11:39:11 CST)
- AW: FATAL ERROR: error parsing config file while executing <feff> Norman Geist (Mon Nov 10 2014 - 00:56:24 CST)
  - Re: AW: FATAL ERROR: error parsing config file while executing <feff> Jim Phillips (Mon Nov 10 2014 - 16:00:19 CST)
Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Bin He (Sat Nov 08 2014 - 01:24:32 CST)
- AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Norman Geist (Mon Nov 10 2014 - 00:53:15 CST)
multiple harmonic constrains Azadeh Alavi (Sat Nov 08 2014 - 01:36:16 CST)
- Re: multiple harmonic constrains Jeff Comer (Sat Nov 08 2014 - 14:54:50 CST)
ffTK problem: OPT.Charges Zeinab Emami (Fri Nov 07 2014 - 09:14:15 CST)
- Re: vmd-l: ffTK problem: OPT.Charges Mayne, Christopher G (Fri Nov 07 2014 - 10:51:57 CST)
  - Re: Re: vmd-l: ffTK problem: OPT.Charges Zeinab Emami (Fri Nov 07 2014 - 11:13:04 CST)
CUDA Fatal Error While Trying to Run Under Windows 8.1 Justin Sanders (Thu Nov 06 2014 - 12:01:58 CST)
- Re: CUDA Fatal Error While Trying to Run Under Windows 8.1 Branko (Thu Nov 06 2014 - 12:15:59 CST)
- Re: CUDA Fatal Error While Trying to Run Under Windows 8.1 Jim Phillips (Thu Nov 06 2014 - 13:00:35 CST)
NAMD on SLURM Abhishek TYAGI (Wed Nov 05 2014 - 23:30:20 CST)
- Re: NAMD on SLURM Mitchell Gleed (Wed Nov 12 2014 - 12:57:16 CST)
  - Re: NAMD on SLURM Abhishek TYAGI (Wed Nov 12 2014 - 21:07:16 CST)
Multiple input and output files Debashis Kundu (Wed Nov 05 2014 - 20:20:37 CST)
- å´”å¹¼æ¬ è‡ªåŠ¨å›žå¤: Multiple input and output files cuiyoutian_at_163.com (Wed Nov 05 2014 - 20:20:37 CST)
- Re: Multiple input and output files Axel Kohlmeyer (Wed Nov 05 2014 - 21:51:44 CST)
- Re: Multiple input and output files Josh Vermaas (Wed Nov 05 2014 - 20:54:02 CST)
  - Re: Multiple input and output files Jim Phillips (Thu Nov 06 2014 - 12:50:36 CST)
1-5 Intramolecular repulsions Rebecca Lindsey (Wed Nov 05 2014 - 11:54:40 CST)
- Re: 1-5 Intramolecular repulsions Kenno Vanommeslaeghe (Wed Nov 05 2014 - 12:33:12 CST)
  - Re: 1-5 Intramolecular repulsions Jeffrey Potoff (Wed Nov 05 2014 - 12:51:02 CST)
  - Re: 1-5 Intramolecular repulsions rocwhite168 (Wed Nov 05 2014 - 13:02:55 CST)
colvars fatal error Leili Zhang (Tue Nov 04 2014 - 22:44:05 CST)
- Re: colvars fatal error JÃ©rÃ´me HÃ©nin (Wed Nov 05 2014 - 02:54:43 CST)
- NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272 Thomas C. Bishop (Wed Nov 05 2014 - 09:48:15 CST)
  - AW: NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272 Norman Geist (Thu Nov 06 2014 - 01:43:36 CST)
  - Re: NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272 Thomas C. Bishop (Tue Nov 11 2014 - 12:41:11 CST)
vdW-only fep between two ions Christopher Rowley (Tue Nov 04 2014 - 14:43:08 CST)
harmonic restraints between multiple atom pairs Neelanjana Sengupta (Mon Nov 03 2014 - 22:42:33 CST)
- RE: harmonic restraints between multiple atom pairs Tristan Croll (Mon Nov 03 2014 - 23:20:09 CST)
explicit membrane in implicit solvent Gisella Alfonsino (Mon Nov 03 2014 - 05:00:36 CST)
- Re: explicit membrane in implicit solvent Kenno Vanommeslaeghe (Mon Nov 03 2014 - 10:46:24 CST)
Why RDF increases as r increase instead of constant Nifeng Guo hui (Sat Nov 01 2014 - 17:07:32 CDT)
- Re: Why RDF increases as r increase instead of constant Kenno Vanommeslaeghe (Sun Nov 02 2014 - 12:38:04 CST)
  - Re: Why RDF increases as r increase instead of constant Kenno Vanommeslaeghe (Sun Nov 02 2014 - 18:25:41 CST)
- Re: Why RDF increases as r increase instead of constant Arash Azari (Mon Nov 03 2014 - 01:32:27 CST)
Reg: dielectric constant calculations in NAMD Akshay Bhatnagar (Fri Oct 31 2014 - 00:51:24 CDT)
Mechanical Properties of protein chin chun (Thu Oct 30 2014 - 19:18:11 CDT)
- Re: Mechanical Properties of protein Maxim Belkin (Thu Oct 30 2014 - 20:27:58 CDT)
SMD constant velocity not constant Charles Whidborne (Wed Oct 29 2014 - 19:25:08 CDT)
- Re: SMD constant velocity not constant Axel Kohlmeyer (Wed Oct 29 2014 - 20:04:28 CDT)
Dioxygen params charmm36 Francesco Pietra (Wed Oct 29 2014 - 16:27:17 CDT)
namd ibverbs compile target Bennion, Brian (Tue Oct 28 2014 - 18:04:52 CDT)
Carma v.1.4 released. Nicholas M Glykos (Mon Oct 27 2014 - 06:09:24 CDT)
jeremy adler jeremy adler (Thu Oct 23 2014 - 06:21:43 CDT)
Reg: error in log file Akshay Bhatnagar (Tue Oct 21 2014 - 20:36:48 CDT)
- Re: Reg: error in log file Jim Phillips (Thu Oct 30 2014 - 10:46:01 CDT)
Improving MDFF results Kevin C Chan (Mon Oct 20 2014 - 22:15:59 CDT)
- RE: Improving MDFF results Tristan Croll (Tue Oct 21 2014 - 00:36:21 CDT)
  - Re: Improving MDFF results Kevin Chun Chan (Tue Oct 21 2014 - 10:56:00 CDT)
    - Re: Improving MDFF results Tristan Croll (Tue Oct 21 2014 - 14:22:31 CDT)
running a calculation during simulation btreece_at_andrew.cmu.edu (Mon Oct 20 2014 - 16:08:12 CDT)
- Re: running a calculation during simulation Josh Vermaas (Mon Oct 20 2014 - 16:38:57 CDT)
- Re: running a calculation during simulation Maxim Belkin (Mon Oct 20 2014 - 18:00:03 CDT)
- Re: running a calculation during simulation Ajasja LjubetiÄ (Tue Oct 21 2014 - 02:52:21 CDT)
  - Re: running a calculation during simulation JÃ©rÃ´me HÃ©nin (Tue Oct 21 2014 - 04:03:13 CDT)
Graphene simualtion Abhishek TYAGI (Mon Oct 20 2014 - 03:28:51 CDT)
AW: wrapping in two dimensions Norman Geist (Mon Oct 20 2014 - 01:14:02 CDT)
Replica Exchange Simulation in NAMD Precompiled binary in single node. Nizar Masbukhin (Thu Oct 16 2014 - 17:09:05 CDT)
wrapping in two dimensions Maria Bykhovskaia (Thu Oct 16 2014 - 15:33:34 CDT)
- AW: wrapping in two dimensions Norman Geist (Fri Oct 17 2014 - 02:21:07 CDT)
AW: velocity manipulation Norman Geist (Thu Oct 16 2014 - 08:26:37 CDT)
AW: velocity manipulation Norman Geist (Thu Oct 16 2014 - 08:11:59 CDT)
velocity manipulation mostafa raeesi (Thu Oct 16 2014 - 06:37:02 CDT)
- AW: velocity manipulation Norman Geist (Thu Oct 16 2014 - 07:27:28 CDT)
- Re: velocity manipulation Axel Kohlmeyer (Thu Oct 16 2014 - 08:21:17 CDT)
  - Re: velocity manipulation Ajasja LjubetiÄ (Thu Oct 16 2014 - 08:24:34 CDT)
ffTK problem: initial parameter file is void of of atoms! Zeinab Emami (Thu Oct 16 2014 - 04:15:55 CDT)
ffTK problem: initial parameter fiel is viod of atoms! Zeinab Emami (Wed Oct 15 2014 - 07:42:57 CDT)
- Re: ffTK problem: initial parameter fiel is viod of atoms! Mayne, Christopher G (Mon Oct 20 2014 - 09:55:55 CDT)
  - Re: Re: ffTK problem: initial parameter fiel is viod of atoms! Zeinab Emami (Mon Oct 20 2014 - 11:33:25 CDT)
    - Re: Re: ffTK problem: initial parameter fiel is viod of atoms! Mayne, Christopher G (Mon Oct 20 2014 - 11:45:39 CDT)
VRPN cannot connect to Falcon George Patargias (Wed Oct 15 2014 - 04:58:11 CDT)
NAMD and usable FFs Francesco Pietra (Wed Oct 15 2014 - 04:34:31 CDT)
- Re: NAMD and usable FFs Josh Vermaas (Wed Oct 15 2014 - 09:20:08 CDT)
  - Re: NAMD and usable FFs Francesco Pietra (Thu Oct 16 2014 - 12:59:10 CDT)
- Re: NAMD and usable FFs Kenno Vanommeslaeghe (Thu Oct 16 2014 - 13:37:11 CDT)
colvars replica exchange oddity JC Gumbart (Tue Oct 14 2014 - 22:27:07 CDT)
VRPN compilation error George Patargias (Tue Oct 14 2014 - 08:43:59 CDT)
- Re: VRPN compilation error Axel Kohlmeyer (Tue Oct 14 2014 - 08:54:12 CDT)
Performance difference of prcompiled binary VS source code Nizar Masbukhin (Mon Oct 13 2014 - 19:23:43 CDT)
MPICH 3 with Namd2/Charm Daniel Strahs (Mon Oct 13 2014 - 18:04:45 CDT)
long running sim dies Thomas C. Bishop (Mon Oct 13 2014 - 08:29:43 CDT)
- Re: long running sim dies Tristan Croll (Mon Oct 13 2014 - 14:36:37 CDT)
- Re: long running sim dies ransun (Mon Oct 13 2014 - 09:12:33 CDT)
Re: vmd-l: making psf files Zeinab Emami (Mon Oct 13 2014 - 04:55:06 CDT)
- Re: Re: vmd-l: making psf files Kenno Vanommeslaeghe (Mon Oct 13 2014 - 12:18:31 CDT)
Reï¼štutorial-l: Protein structure distorted after Energy minimization with NAMD sunyeping (Wed Oct 08 2014 - 21:58:02 CDT)
Umbrella sampling tilt with respect to Z-axis Mitchell Gleed (Wed Oct 08 2014 - 15:38:29 CDT)
- Re: Umbrella sampling tilt with respect to Z-axis Giacomo Fiorin (Wed Oct 08 2014 - 15:45:04 CDT)
  - Re: Umbrella sampling tilt with respect to Z-axis Mitchell Gleed (Wed Oct 08 2014 - 18:07:00 CDT)
    - Re: Umbrella sampling tilt with respect to Z-axis Aron Broom (Wed Oct 08 2014 - 18:54:44 CDT)
question about '+devices' ukulililixl (Wed Oct 08 2014 - 01:06:50 CDT)
- AW: question about '+devices' Norman Geist (Wed Oct 08 2014 - 02:13:08 CDT)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Tue Oct 07 2014 - 11:30:07 CDT)
String method in NAMD 2.10b1? Jenny lou (Mon Oct 06 2014 - 12:58:17 CDT)
Parameter colvars Z (Mon Oct 06 2014 - 05:26:21 CDT)
- Re: Parameter colvars Giacomo Fiorin (Mon Oct 06 2014 - 05:45:41 CDT)
  - Re: Parameter colvars Z (Mon Oct 06 2014 - 05:56:07 CDT)
- Re: Parameter colvars Z (Mon Oct 06 2014 - 06:55:44 CDT)
Does NAMD have some way to test the result? ukulililixl (Fri Oct 03 2014 - 21:50:52 CDT)
- Re: Does NAMD have some way to test the result? Axel Kohlmeyer (Fri Oct 03 2014 - 22:17:05 CDT)
  - Re: Does NAMD have some way to test the result? JÃ©rÃ´me HÃ©nin (Sat Oct 04 2014 - 04:20:57 CDT)
Newbie GPU user, please help with my submission line Jose Borreguero (Thu Oct 02 2014 - 14:03:24 CDT)
Re: Self-Assemble Monolayer--Periodic Boundary Conditions Natnael Doilicho (Wed Oct 01 2014 - 16:14:52 CDT)
How to Amend a PBD file for NAMD Zeinab Emami (Wed Oct 01 2014 - 09:27:15 CDT)
AW: vmd-l: Stray PME grid Norman Geist (Wed Oct 01 2014 - 02:27:31 CDT)
FATAL ERROR: Setting parameter colvars from script failed! Mihaela Drenscko (Tue Sep 30 2014 - 09:27:18 CDT)
- Re: FATAL ERROR: Setting parameter colvars from script failed! JÃ©rÃ´me HÃ©nin (Tue Sep 30 2014 - 10:17:02 CDT)
  - Re: FATAL ERROR: Setting parameter colvars from script failed! JÃ©rÃ´me HÃ©nin (Tue Sep 30 2014 - 13:04:27 CDT)
  - Re: FATAL ERROR: Setting parameter colvars from script failed! JÃ©rÃ´me HÃ©nin (Tue Sep 30 2014 - 13:28:48 CDT)
Folic acid parameters Haleh a (Tue Sep 30 2014 - 08:44:38 CDT)
- Re: Folic acid parameters Fotis Baltoumas (Tue Sep 30 2014 - 10:06:43 CDT)
  - Re: Folic acid parameters Kenno Vanommeslaeghe (Tue Sep 30 2014 - 11:37:03 CDT)
    - Re: Folic acid parameters Haleh a (Wed Oct 01 2014 - 01:42:20 CDT)
- Re: Folic acid parameters Kenno Vanommeslaeghe (Tue Sep 30 2014 - 10:43:21 CDT)
Self-Assemble Monolayer--Periodic Boundary Conditions Natnael Doilicho (Mon Sep 29 2014 - 18:03:18 CDT)
- AW: Self-Assemble Monolayer--Periodic Boundary Conditions Norman Geist (Tue Sep 30 2014 - 01:38:57 CDT)
PCL dcd files Mihaela Drenscko (Mon Sep 29 2014 - 11:09:40 CDT)
- Fwd: PCL dcd files Mihaela Drenscko (Mon Sep 29 2014 - 11:38:30 CDT)
  - Re: PCL dcd files Giacomo Fiorin (Mon Sep 29 2014 - 12:10:07 CDT)
    - Re: PCL dcd files Niklaus Johner (Tue Sep 30 2014 - 01:15:25 CDT)
Molecular Dynamics of Rigid Linear Molecules in NAMD. Javad Noroozi (Sun Sep 28 2014 - 00:44:28 CDT)
- Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Mike Makowski (Sun Sep 28 2014 - 03:03:10 CDT)
  - Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Mike Makowski (Sun Sep 28 2014 - 06:50:36 CDT)
SMD pulling speed Charles Whidborne (Sat Sep 27 2014 - 20:45:48 CDT)
- Re: SMD pulling speed Giacomo Fiorin (Sat Sep 27 2014 - 21:16:15 CDT)
namd coulomb conversion factor Mohan maruthi sena (Sat Sep 27 2014 - 01:09:43 CDT)
Reg: minimization Akshay Bhatnagar (Wed Sep 24 2014 - 23:35:16 CDT)
- Re: Reg: minimization Axel Kohlmeyer (Wed Sep 24 2014 - 23:44:35 CDT)
  - Re: Reg: minimization Akshay Bhatnagar (Thu Sep 25 2014 - 04:51:52 CDT)
  - Re: Reg: minimization Akshay Bhatnagar (Thu Sep 25 2014 - 04:52:40 CDT)
    - AW: Reg: minimization Norman Geist (Thu Sep 25 2014 - 05:23:26 CDT)
getting different dihedral energy with two identical backbones Joyce Yang (Wed Sep 24 2014 - 16:45:52 CDT)
- Re: getting different dihedral energy with two identical backbones Jim Phillips (Fri Sep 26 2014 - 17:18:24 CDT)
  - Re: getting different dihedral energy with two identical backbones Joyce Yang (Mon Sep 29 2014 - 21:15:54 CDT)
expected speed up after fixing atoms? Jose Borreguero (Wed Sep 24 2014 - 12:44:48 CDT)
- Re: expected speed up after fixing atoms? Aron Broom (Wed Sep 24 2014 - 13:10:45 CDT)
  - Re: expected speed up after fixing atoms? Jose Borreguero (Wed Sep 24 2014 - 13:41:02 CDT)
- Re: expected speed up after fixing atoms? Kenno Vanommeslaeghe (Wed Sep 24 2014 - 14:06:46 CDT)
Problem with running namdenergy plugin from text interface zeynab mohamad hoseyni (Mon Sep 22 2014 - 14:53:04 CDT)
- Re: Problem with running namdenergy plugin from text interface Josh Vermaas (Mon Sep 22 2014 - 15:09:10 CDT)
  - Re: Problem with running namdenergy plugin from text interface zeynab mohamad hoseyni (Mon Sep 22 2014 - 22:29:26 CDT)
which namd versions compatible with CUDA 5.5 and other CUDA woes Robert Wohlhueter (Mon Sep 22 2014 - 13:39:19 CDT)
- Re: which namd versions compatible with CUDA 5.5 and other CUDA woes Jim Phillips (Fri Sep 26 2014 - 17:25:29 CDT)
  - Re: which namd versions compatible with CUDA 5.5 and other CUDA woes Robert Wohlhueter (Sun Sep 28 2014 - 12:00:17 CDT)
Re: Is there any point in running NAMD over an ethernet-linked cluster? Nicholas M Glykos (Sun Sep 21 2014 - 13:21:53 CDT)
- Re: Is there any point in running NAMD over an ethernet-linked cluster? Douglas Houston (Mon Sep 22 2014 - 00:23:41 CDT)
  - Re: Is there any point in running NAMD over an ethernet-linked cluster? Axel Kohlmeyer (Mon Sep 22 2014 - 01:22:11 CDT)
    - Re: Is there any point in running NAMD over an ethernet-linked cluster? Nicholas M Glykos (Mon Sep 22 2014 - 03:40:59 CDT)
Simulation Do not Run in the Cluster Roy Fernando (Sun Sep 21 2014 - 12:16:44 CDT)
Implicit solvent lipid bilayer simulation in NAMD. Subbarao Kanchi (Wed Sep 17 2014 - 12:04:44 CDT)
- Re: Implicit solvent lipid bilayer simulation in NAMD. Siva Dasetty (Wed Sep 17 2014 - 13:23:53 CDT)
  - Re: Implicit solvent lipid bilayer simulation in NAMD. Subbarao Kanchi (Wed Sep 17 2014 - 13:41:34 CDT)
simulation options available with GPU Ana Celia Vila Verde (Tue Sep 16 2014 - 02:52:51 CDT)
Constraining two sets of atoms Natnael Doilicho (Tue Sep 16 2014 - 12:06:38 CDT)
simulation options available with GPU Ana Celia Vila Verde (Tue Sep 16 2014 - 02:58:28 CDT)
Setting constraints for SMD simulation Charles Whidborne (Mon Sep 15 2014 - 20:20:39 CDT)
Annealing process of silica with excluded block Marzieh Alishahi (Fri Sep 12 2014 - 10:22:51 CDT)
- Re: Annealing process of silica with excluded block Jeff Comer (Mon Sep 15 2014 - 09:30:57 CDT)
  - Re: Annealing process of silica with excluded block Marzieh Alishahi (Mon Sep 15 2014 - 09:40:21 CDT)
Qh Lurong Pan (Thu Sep 11 2014 - 08:22:22 CDT)
Unsubscribe Katherine Parra (Wed Sep 10 2014 - 09:12:24 CDT)
I would like to unsubscribe Maria Kopp (Wed Sep 10 2014 - 09:04:54 CDT)
- Re: I would like to unsubscribe MEHRAN MB (Wed Sep 10 2014 - 09:19:54 CDT)
- Re: I would like to unsubscribe Giacomo Fiorin (Wed Sep 10 2014 - 09:21:11 CDT)
- Re: I would like to unsubscribe Ajasja LjubetiÄ (Wed Sep 10 2014 - 10:03:21 CDT)
Colvars simulation running slow? Tristan Croll (Tue Sep 09 2014 - 20:31:06 CDT)
- Re: Colvars simulation running slow? JÃ©rÃ´me HÃ©nin (Wed Sep 10 2014 - 02:13:00 CDT)
  - RE: Colvars simulation running slow? Tristan Croll (Wed Sep 10 2014 - 17:15:35 CDT)
    - RE: Colvars simulation running slow? Tristan Croll (Wed Sep 10 2014 - 19:51:15 CDT)
    - Re: Colvars simulation running slow? Ajasja LjubetiÄ (Wed Sep 10 2014 - 19:58:48 CDT)
GBIS using CUDA enabled NAMD Siva Dasetty (Tue Sep 09 2014 - 18:59:01 CDT)
- Re: GBIS using CUDA enabled NAMD David Hardy (Wed Sep 10 2014 - 14:46:22 CDT)
- Re: GBIS using CUDA enabled NAMD Jim Phillips (Wed Sep 10 2014 - 16:32:32 CDT)
  - Re: GBIS using CUDA enabled NAMD Siva Dasetty (Wed Sep 17 2014 - 09:36:03 CDT)
[ANN] MDTraj 1.0: Trajectory Analysis in Python Robert McGibbon (Mon Sep 08 2014 - 17:19:00 CDT)
- Re: [ANN] MDTraj 1.0: Trajectory Analysis in Python Ivan Gregoretti (Tue Sep 09 2014 - 12:09:49 CDT)
Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 09:04:32 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Branko (Mon Sep 08 2014 - 09:13:35 CDT)
  - Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 09:38:31 CDT)
  - Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 15:27:12 CDT)
    - Re: Unable to read corrupted binary DCD trajectory file Kenno Vanommeslaeghe (Mon Sep 08 2014 - 16:38:48 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Andreas Förster (Mon Sep 08 2014 - 09:29:51 CDT)
  - Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 09:43:47 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Gergely Gyimesi (Mon Sep 08 2014 - 09:51:33 CDT)
GBIS CUDA not yet compatible with fixed atoms Siva Dasetty (Fri Sep 05 2014 - 10:03:12 CDT)
- Re: GBIS CUDA not yet compatible with fixed atoms Jim Phillips (Fri Sep 05 2014 - 15:16:04 CDT)
  - Re: GBIS CUDA not yet compatible with fixed atoms Siva Dasetty (Fri Sep 05 2014 - 15:24:45 CDT)
    - Re: GBIS CUDA not yet compatible with fixed atoms Aron Broom (Fri Sep 05 2014 - 16:50:39 CDT)
    - Re: GBIS CUDA not yet compatible with fixed atoms Siva Dasetty (Fri Sep 05 2014 - 18:01:13 CDT)
SASA calculation Siva Dasetty (Thu Sep 04 2014 - 09:03:56 CDT)
FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Sandhyaa Subramanian (Wed Sep 03 2014 - 02:34:06 CDT)
Question to NAMD source Norman Geist (Thu Sep 04 2014 - 08:02:31 CDT)
- Re: Question to NAMD source Jim Phillips (Thu Sep 04 2014 - 11:25:48 CDT)
  - AW: Question to NAMD source Norman Geist (Fri Sep 05 2014 - 01:32:29 CDT)
Alignment Zeinab Emami (Thu Sep 04 2014 - 07:12:14 CDT)
- Re: Alignment Axel Kohlmeyer (Thu Sep 04 2014 - 07:53:23 CDT)
efficient way to apply time-dependent electric field Azadeh Alavi (Thu Sep 04 2014 - 05:38:12 CDT)
- Re: efficient way to apply time-dependent electric field Jim Phillips (Thu Sep 04 2014 - 11:18:00 CDT)
computing forces on atoms by postprocessing a dcd file generated with FEP enabled Harris, Robert C. (Wed Sep 03 2014 - 14:05:40 CDT)
INCONSISTENCY messages and minimization in toturial 1-2-sphere Yan Zhou (Wed Sep 03 2014 - 03:14:30 CDT)
FEP, Ewald size-dependence charge correction Sebastian Stolzenberg (Tue Sep 02 2014 - 15:12:17 CDT)
- Re: FEP, Ewald size-dependence charge correction Sebastian Stolzenberg (Sun Sep 07 2014 - 10:23:17 CDT)
  - Re: FEP, Ewald size-dependence charge correction Sebastian Stolzenberg (Fri Sep 12 2014 - 13:21:10 CDT)
    - Re: FEP, Ewald size-dependence charge correction JC Gumbart (Sat Sep 13 2014 - 18:38:44 CDT)
FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Sandhyaa Subramanian (Sat Aug 30 2014 - 09:06:14 CDT)
- RE: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Tristan Croll (Tue Sep 02 2014 - 17:27:20 CDT)
  - RE: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Tristan Croll (Wed Sep 03 2014 - 02:26:27 CDT)
    - Re: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Sandhyaa Subramanian (Wed Sep 03 2014 - 02:37:32 CDT)
problems running ABF simulation Charles Whidborne (Tue Sep 02 2014 - 00:37:40 CDT)
- Re: problems running ABF simulation Giacomo Fiorin (Tue Sep 02 2014 - 02:45:26 CDT)
Re: Fixing atoms while equilibration Siva Dasetty (Mon Sep 01 2014 - 07:33:57 CDT)
- Re: Fixing atoms while equilibration Axel Kohlmeyer (Mon Sep 01 2014 - 07:48:34 CDT)
  - Re: Fixing atoms while equilibration Siva Dasetty (Mon Sep 01 2014 - 08:07:59 CDT)
    - Re: Fixing atoms while equilibration Axel Kohlmeyer (Mon Sep 01 2014 - 08:14:37 CDT)
    - Re: Fixing atoms while equilibration Kenno Vanommeslaeghe (Mon Sep 01 2014 - 10:52:07 CDT)
problem in calculating binding energy using MMGBSA with namd-2.9 Shailesh Pandey (Mon Sep 01 2014 - 07:31:34 CDT)
Reg: solvation in DMSO Akshay Bhatnagar (Mon Sep 01 2014 - 00:01:44 CDT)
- Fwd: Reg: solvation in DMSO Akshay Bhatnagar (Wed Sep 03 2014 - 02:36:04 CDT)
  - Re: Fwd: Reg: solvation in DMSO Kenno Vanommeslaeghe (Wed Sep 03 2014 - 14:43:59 CDT)
restraining bonds Neelanjana Sengupta (Sun Aug 31 2014 - 23:50:24 CDT)
- RE: restraining bonds Tristan Croll (Mon Sep 01 2014 - 00:45:22 CDT)
  - RE: restraining bonds Tristan Croll (Mon Sep 01 2014 - 00:57:28 CDT)
  - RE: restraining bonds Tristan Croll (Mon Sep 01 2014 - 01:09:05 CDT)
    - Re: restraining bonds Kenno Vanommeslaeghe (Mon Sep 01 2014 - 10:37:17 CDT)
    - Re: restraining bonds Kenno Vanommeslaeghe (Tue Sep 02 2014 - 11:04:37 CDT)
NAMD energy minimization Siva Dasetty (Sun Aug 31 2014 - 14:30:56 CDT)
- Re: NAMD energy minimization Axel Kohlmeyer (Sun Aug 31 2014 - 14:51:10 CDT)
RDF calculation of crystal system Fatemeh Omidbeygi (Sat Aug 30 2014 - 00:41:02 CDT)
- Re: RDF calculation of crystal system Axel Kohlmeyer (Sat Aug 30 2014 - 01:49:16 CDT)
Fixing atoms while equilibration Siva Dasetty (Fri Aug 29 2014 - 20:12:21 CDT)
- AW: Fixing atoms while equilibration Norman Geist (Mon Sep 01 2014 - 02:26:11 CDT)
Re: ibverb&&smp build NAMD ukulililixl (Fri Aug 29 2014 - 06:41:21 CDT)
- AW: ibverb&&smp build NAMD Norman Geist (Mon Sep 01 2014 - 02:17:13 CDT)
Assessing convergence in FEP calculations Gianluca Interlandi (Thu Aug 28 2014 - 14:00:08 CDT)
Combining interleaved and top posting is considered harmful. Nicholas M Glykos (Thu Aug 28 2014 - 11:11:40 CDT)
- Re: Combining interleaved and top posting is considered harmful. Jim Phillips (Thu Aug 28 2014 - 11:29:10 CDT)
Set exact molarity in cell Stephan Grein (Thu Aug 28 2014 - 09:08:42 CDT)
ibverb&&smp build NAMD ukulililixl (Thu Aug 28 2014 - 04:30:47 CDT)
- AW: ibverb&&smp build NAMD Norman Geist (Thu Aug 28 2014 - 05:25:13 CDT)
(no subject) BIPLAB NANDI (Wed Aug 27 2014 - 22:13:06 CDT)
- Re: Gianluca Interlandi (Thu Aug 28 2014 - 00:16:37 CDT)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Aug 27 2014 - 13:05:05 CDT)
Window for FEP calculations Gianluca Interlandi (Tue Aug 26 2014 - 19:35:33 CDT)
NAMD 2.10b1 CUDA PME offload Norman Geist (Tue Aug 26 2014 - 09:25:48 CDT)
- Re: NAMD 2.10b1 CUDA PME offload Jim Phillips (Tue Aug 26 2014 - 10:22:48 CDT)
- AW: NAMD 2.10b1 CUDA PME offload Norman Geist (Tue Aug 26 2014 - 10:24:50 CDT)
Metadynamics test along eigenvector Floquet Nicolas (Tue Aug 26 2014 - 02:58:00 CDT)
- Re: Metadynamics test along eigenvector Giacomo Fiorin (Tue Aug 26 2014 - 10:07:34 CDT)
(no subject) ukulililixl (Tue Aug 26 2014 - 01:22:20 CDT)
- Re: Jim Phillips (Tue Aug 26 2014 - 10:38:36 CDT)
Siginificant speedup by updating nvidia driver Norman Geist (Mon Aug 25 2014 - 11:06:38 CDT)
Nucleic acid stains parameters SebastiÃ¡n GutiÃ©rrez (Mon Aug 25 2014 - 10:37:04 CDT)
- Re: Nucleic acid stains parameters Kenno Vanommeslaeghe (Mon Aug 25 2014 - 10:56:26 CDT)
Metadynamics with eigenvector Nicolas Floquet (Mon Aug 25 2014 - 09:40:06 CDT)
- Re: Metadynamics with eigenvector Giacomo Fiorin (Mon Aug 25 2014 - 10:17:22 CDT)
NAMD 2.10b1 released Jim Phillips (Mon Aug 25 2014 - 07:49:51 CDT)
question in NAMD with icc & cuda ukulililixl (Mon Aug 25 2014 - 06:40:48 CDT)
ABF hBond Charles Whidborne (Mon Aug 25 2014 - 02:52:45 CDT)
- Re: ABF hBond Giacomo Fiorin (Mon Aug 25 2014 - 10:18:12 CDT)
AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Norman Geist (Fri Aug 22 2014 - 08:21:25 CDT)
- Re: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Maxime Boissonneault (Fri Aug 22 2014 - 08:22:43 CDT)
  - AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Norman Geist (Fri Aug 22 2014 - 08:56:32 CDT)
FATAL ERROR: PME offload requires exactly one CUDA device per process. Maxime Boissonneault (Fri Aug 22 2014 - 06:40:06 CDT)
Re: NAMD 2.10 Manual Ajasja LjubetiÄ (Fri Aug 22 2014 - 03:30:05 CDT)
- AW: NAMD 2.10 Manual Norman Geist (Fri Aug 22 2014 - 08:46:07 CDT)
NAMD 2.10 Manual Norman Geist (Fri Aug 22 2014 - 03:14:47 CDT)
Installation Protocol of NAMD on Linux Cluster Viswanath Pasumarthi (Thu Aug 21 2014 - 14:46:27 CDT)
SMP vs Multicore Maxime Boissonneault (Thu Aug 21 2014 - 09:26:43 CDT)
Fwd: [External] Boost value in aMD simulation Thomas Evangelidis (Thu Aug 21 2014 - 06:05:05 CDT)
- Re: [External] Boost value in aMD simulation James Starlight (Fri Aug 22 2014 - 11:54:05 CDT)
wrapping a protein Maria Bykhovskaia (Wed Aug 20 2014 - 17:40:30 CDT)
- Re: wrapping a protein Maxim Belkin (Wed Aug 20 2014 - 17:53:46 CDT)
Accelerated molecular dynamics: Energy value in output file Kapil jain (Tue Aug 19 2014 - 23:53:20 CDT)
using CHARMM-format Amber parameters in NAMD Basheer Subei (Tue Aug 19 2014 - 19:16:43 CDT)
- Re: using CHARMM-format Amber parameters in NAMD Mike Makowski (Tue Aug 19 2014 - 23:34:13 CDT)
  - Re: using CHARMM-format Amber parameters in NAMD Kenno Vanommeslaeghe (Wed Aug 20 2014 - 10:27:20 CDT)
    - Re: using CHARMM-format Amber parameters in NAMD Basheer (Wed Aug 20 2014 - 22:15:22 CDT)
"Beefier" benchmark Maxime Boissonneault (Tue Aug 19 2014 - 10:48:30 CDT)
- Re: "Beefier" benchmark Phil Greer (Tue Aug 19 2014 - 11:10:28 CDT)
  - Re: "Beefier" benchmark Maxime Boissonneault (Tue Aug 19 2014 - 11:14:31 CDT)
  - Re: "Beefier" benchmark Aron Broom (Tue Aug 19 2014 - 11:15:29 CDT)
Fwd: [External] Boost value in aMD simulation Thomas Evangelidis (Tue Aug 19 2014 - 05:24:17 CDT)
- Re: [External] Boost value in aMD simulation James Starlight (Tue Aug 19 2014 - 13:45:58 CDT)
NVT, NPT, order & combination Zeinab Emami (Tue Aug 19 2014 - 03:23:26 CDT)
- Re: NVT, NPT, order & combination Kenno Vanommeslaeghe (Tue Aug 19 2014 - 12:17:27 CDT)
Atom selection in Tcl Force script with Amber partop file Daniel Torrente (Fri Aug 15 2014 - 12:25:49 CDT)
- Re: Atom selection in Tcl Force script with Amber partop file Maxim Belkin (Fri Aug 15 2014 - 16:48:12 CDT)
  - Re: Atom selection in Tcl Force script with Amber partop file Daniel Torrente (Fri Aug 15 2014 - 18:25:23 CDT)
  - Re: Atom selection in Tcl Force script with Amber partop file Daniel Torrente (Fri Aug 15 2014 - 18:21:23 CDT)
    - Re: Atom selection in Tcl Force script with Amber partop file Maxim Belkin (Fri Aug 15 2014 - 18:33:18 CDT)
    - Re: Atom selection in Tcl Force script with Amber partop file Daniel Torrente (Fri Aug 15 2014 - 19:01:23 CDT)
Martini forcefield RBCG and ENM Raul Araya (Fri Aug 15 2014 - 10:05:01 CDT)
Hwo to switch from NPT to NVT Zeinab Emami (Fri Aug 15 2014 - 07:14:05 CDT)
Hwo to switch from NPT to NVT Zeinab Emami (Fri Aug 15 2014 - 07:12:39 CDT)
H-Bond measurements Stephan Grein (Thu Aug 14 2014 - 01:57:40 CDT)
Hybrid MPI + Multicore + Cuda build Maxime Boissonneault (Wed Aug 13 2014 - 11:46:59 CDT)
- AW: Hybrid MPI + Multicore + Cuda build Norman Geist (Thu Aug 14 2014 - 02:13:32 CDT)
  - Re: AW: Hybrid MPI + Multicore + Cuda build Maxime Boissonneault (Thu Aug 14 2014 - 07:19:37 CDT)
Root mean square deviation.......... Gurpreet Kaur Dhindsa (Tue Aug 12 2014 - 12:58:38 CDT)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Tue Aug 12 2014 - 09:31:17 CDT)
NAMD CVS_CUDA ERROR: "all CUDA-capable devices are busy or unavailable" Samuel Bowerman (Mon Aug 11 2014 - 11:50:45 CDT)
Running NAMD via GROMACS topology Mike Makowski (Sun Aug 10 2014 - 17:44:35 CDT)
- Re: Running NAMD via GROMACS topology Mike Makowski (Sun Aug 10 2014 - 18:05:21 CDT)
  - AW: Running NAMD via GROMACS topology Norman Geist (Mon Aug 11 2014 - 00:33:15 CDT)
Unsubscribe Katherine Parra (Sun Aug 10 2014 - 11:30:22 CDT)
(no subject) Shalton Evans (Sat Aug 09 2014 - 23:00:48 CDT)
Energy term in output file of Accelerated dynamics Kapil jain (Fri Aug 08 2014 - 02:14:56 CDT)
- Re: Energy term in output file of Accelerated dynamics Kapil jain (Sun Aug 10 2014 - 21:39:32 CDT)
ABF simulation, free energy to remove a DNA strand Charles Whidborne (Tue Aug 05 2014 - 01:54:14 CDT)
- Re: ABF simulation, free energy to remove a DNA strand JÃ©rÃ´me HÃ©nin (Tue Aug 05 2014 - 03:15:46 CDT)
  - Re: ABF simulation, free energy to remove a DNA strand Thomas C. Bishop (Tue Aug 05 2014 - 10:17:07 CDT)
(no subject) sudipta.mml (Sat Aug 02 2014 - 20:01:46 CDT)
Intermolecular potential energy function in NAMD Viswanath Pasumarthi (Fri Aug 01 2014 - 06:31:21 CDT)
- Re: Intermolecular potential energy function in NAMD Kenno Vanommeslaeghe (Fri Aug 01 2014 - 11:41:46 CDT)
Silent crash NAMD-multicore-CUDA MEHRAN MB (Wed Jul 30 2014 - 17:23:10 CDT)
- Re: Silent crash NAMD-multicore-CUDA Aron Broom (Wed Jul 30 2014 - 17:50:54 CDT)
  - Re: Silent crash NAMD-multicore-CUDA MEHRAN MB (Thu Jul 31 2014 - 18:27:55 CDT)
    - Re: Silent crash NAMD-multicore-CUDA MEHRAN MB (Tue Aug 19 2014 - 11:06:34 CDT)
    - Re: Silent crash NAMD-multicore-CUDA Aron Broom (Tue Aug 19 2014 - 11:17:04 CDT)
Loss of Translational entropy calculation in FEP Daniel Torrente (Wed Jul 30 2014 - 16:57:08 CDT)
+p option on Windows 7 Kukol, Andreas (Wed Jul 30 2014 - 09:56:28 CDT)
Kb, Ktheta values for TIP3P water model Viswanath Pasumarthi (Tue Jul 29 2014 - 16:38:28 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Tue Jul 29 2014 - 17:59:19 CDT)
  - Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Tue Jul 29 2014 - 23:21:58 CDT)
- Re: Kb, Ktheta values for TIP3P water model Maxim Belkin (Mon Aug 11 2014 - 18:05:41 CDT)
Analysis problem (Data vector empty) Stephan Grein (Tue Jul 29 2014 - 04:06:27 CDT)
temperature for lipid-protein assembly Bala subramanian (Mon Jul 28 2014 - 10:19:10 CDT)
- Re: temperature for lipid-protein assembly Kenno Vanommeslaeghe (Mon Jul 28 2014 - 10:57:41 CDT)
  - Re: temperature for lipid-protein assembly Bala subramanian (Mon Jul 28 2014 - 12:06:34 CDT)
Rule of thumb for equilibration Stephan Grein (Mon Jul 28 2014 - 09:45:43 CDT)
- Re: Rule of thumb for equilibration Aron Broom (Mon Jul 28 2014 - 09:59:04 CDT)
segmentation fault in accelMD Anna Modzelewska (Mon Jul 28 2014 - 05:56:05 CDT)
REï¼š The water box shrinks at the start of the MD simulation sunyeping (Sun Jul 27 2014 - 19:19:15 CDT)
The water box shrinks at the start of the MD simulation Zheng Fulu (Sun Jul 27 2014 - 13:53:55 CDT)
The water box shrinks at the start of the MD simulation #ZHENG FULU# (Sun Jul 27 2014 - 06:13:52 CDT)
Fwd: membrane lipid involvement of cholesterol Thomas Evangelidis (Sat Jul 26 2014 - 06:39:30 CDT)
Accelerated MD (aMD) Ramin Ekhteiari (Sat Jul 26 2014 - 06:06:25 CDT)
- Re: Accelerated MD (aMD) Thomas Evangelidis (Sat Jul 26 2014 - 06:38:20 CDT)
- Re: vmd-l: Accelerated MD (aMD) Juan R. Perilla (Sun Jul 27 2014 - 20:23:00 CDT)
membrane lipid involvement of cholesterol Ramin Ekhteiari (Sat Jul 26 2014 - 03:14:38 CDT)
- RE: vmd-l: membrane lipid involvement of cholesterol Richard Wood (Sat Jul 26 2014 - 06:26:59 CDT)
  - RE: vmd-l: membrane lipid involvement of cholesterol Richard Wood (Sat Jul 26 2014 - 09:07:57 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 105 107) Cenk Denktas (Fri Jul 25 2014 - 15:30:40 CDT)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 105 107) Kenno Vanommeslaeghe (Fri Jul 25 2014 - 16:44:15 CDT)
Loading and analysis of DCD file (~300 MB) Stephan Grein (Thu Jul 24 2014 - 06:18:45 CDT)
- Re: Loading and analysis of DCD file (~300 MB) Stephan Grein (Thu Jul 24 2014 - 06:45:54 CDT)
- Re: Loading and analysis of DCD file (~300 MB) tillmann.utesch_at_mailbox.tu-berlin.de (Thu Jul 24 2014 - 07:00:09 CDT)
  - Re: Loading and analysis of DCD file (~300 MB) Stephan Grein (Thu Jul 24 2014 - 07:02:53 CDT)
    - Re: Loading and analysis of DCD file (~300 MB) Ajasja LjubetiÄ (Thu Jul 24 2014 - 09:30:12 CDT)
Reg: LangevinPistonDecay and LangevinPistonPeriod Akshay Bhatnagar (Thu Jul 24 2014 - 02:04:25 CDT)
Re: [External] Boost value in aMD simulation James Starlight (Wed Jul 23 2014 - 14:24:45 CDT)
- Re: [External] Boost value in aMD simulation Thomas Evangelidis (Wed Jul 23 2014 - 15:02:25 CDT)
  - Re: [External] Boost value in aMD simulation James Starlight (Wed Jul 23 2014 - 15:32:53 CDT)
    - Re: [External] Boost value in aMD simulation Thomas Evangelidis (Wed Jul 23 2014 - 16:37:47 CDT)
    - Re: [External] Boost value in aMD simulation James Starlight (Thu Jul 24 2014 - 01:13:09 CDT)
- Re: [External] Boost value in aMD simulation James Starlight (Mon Aug 18 2014 - 03:25:53 CDT)
  - Re: [External] Boost value in aMD simulation Thomas Evangelidis (Mon Aug 18 2014 - 04:21:25 CDT)
    - Re: [External] Boost value in aMD simulation James Starlight (Tue Aug 19 2014 - 04:56:58 CDT)
Boost value in aMD simulation James Starlight (Wed Jul 23 2014 - 06:30:12 CDT)
NAMD_energy_plot sananda chatterjee (Tue Jul 22 2014 - 17:08:56 CDT)
- Re: NAMD_energy_plot Jason Swails (Tue Jul 22 2014 - 17:22:29 CDT)
(no subject) Carlos Navarrro Retamal (Tue Jul 22 2014 - 11:43:10 CDT)
- Re: Kenno Vanommeslaeghe (Tue Jul 22 2014 - 11:58:25 CDT)
(no subject) Mitul Saha (Tue Jul 22 2014 - 11:27:04 CDT)
- Re: Aaron Larsen (Tue Jul 22 2014 - 11:38:27 CDT)
  - Re: JÃ©rÃ´me HÃ©nin (Tue Jul 22 2014 - 11:57:54 CDT)
ABF/colvar error in NAMD2.9 Harish Vashisth (Tue Jul 22 2014 - 11:23:13 CDT)
- Re: ABF/colvar error in NAMD2.9 JÃ©rÃ´me HÃ©nin (Tue Jul 22 2014 - 11:29:47 CDT)
  - Re: ABF/colvar error in NAMD2.9 Niklaus Johner (Tue Jul 22 2014 - 13:32:12 CDT)
    - Re: ABF/colvar error in NAMD2.9 Harish Vashisth (Tue Jul 22 2014 - 14:39:15 CDT)
- Re: ABF/colvar error in NAMD2.9 Aron Broom (Tue Jul 22 2014 - 11:30:49 CDT)
  - Re: ABF/colvar error in NAMD2.9 JÃ©rÃ´me HÃ©nin (Tue Jul 22 2014 - 11:56:06 CDT)
Subject: RE: Re:Subject: Re: Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Tue Jul 22 2014 - 06:28:57 CDT)
Cost of a colvar calculation George Patargias (Tue Jul 22 2014 - 06:27:52 CDT)
- Re: Cost of a colvar calculation JÃ©rÃ´me HÃ©nin (Tue Jul 22 2014 - 06:56:42 CDT)
  - Re: Cost of a colvar calculation Ivan Gregoretti (Tue Jul 22 2014 - 07:33:14 CDT)
- Re: Cost of a colvar calculation Jo, Sunhwan (Tue Jul 22 2014 - 13:06:12 CDT)
  - Re: Cost of a colvar calculation Giacomo Fiorin (Tue Jul 22 2014 - 17:31:23 CDT)
    - Re: Cost of a colvar calculation Jo, Sunhwan (Tue Jul 22 2014 - 19:02:20 CDT)
Subject: Re: Subject: Re: Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Tue Jul 22 2014 - 05:04:09 CDT)
- 2-residue patch for Asn-Lys side chain amide bond Kenno Vanommeslaeghe (Fri Jul 25 2014 - 12:20:46 CDT)
Inquiry about forceConstant Mo Chen (Mon Jul 21 2014 - 15:03:30 CDT)
- Re: Inquiry about forceConstant Aron Broom (Mon Jul 21 2014 - 15:12:06 CDT)
  - Re: Inquiry about forceConstant Mo Chen (Mon Jul 21 2014 - 15:23:06 CDT)
    - Re: Inquiry about forceConstant Mo Chen (Mon Jul 21 2014 - 16:57:15 CDT)
    - Re: Inquiry about forceConstant JÃ©rÃ´me HÃ©nin (Tue Jul 22 2014 - 04:37:30 CDT)
Reg: deciding cell basis vector Akshay Bhatnagar (Mon Jul 21 2014 - 08:57:57 CDT)
- Re: Reg: deciding cell basis vector Aron Broom (Mon Jul 21 2014 - 12:39:39 CDT)
exchange force constants Lu Hong (Mon Jul 21 2014 - 08:50:24 CDT)
- Re: exchange force constants Sunhwan Jo (Mon Jul 21 2014 - 09:30:08 CDT)
  - RE: exchange force constants Lu Hong (Mon Jul 21 2014 - 11:25:25 CDT)
Calculating the force needed to constrain a protein Shane.OMahony (Fri Jul 18 2014 - 11:18:05 CDT)
- Re: Calculating the force needed to constrain a protein Maxim Belkin (Fri Jul 18 2014 - 11:43:27 CDT)
School on Molecular Dynamics with NAMD and LAMMPS in Philadelphia, August 18-22 2014 Axel Kohlmeyer (Thu Jul 17 2014 - 14:48:33 CDT)
running Linux-x86_64-multicore precompiled version at 2 hexa-core CPUs? Andras Borosy (Thu Jul 17 2014 - 09:27:46 CDT)
- Re: running Linux-x86_64-multicore precompiled version at 2 hexa-core CPUs? Axel Kohlmeyer (Thu Jul 17 2014 - 09:35:59 CDT)
NAMD/MIC & CUDA on Stampede Jeffery Klauda (Wed Jul 16 2014 - 13:28:27 CDT)
- Re: NAMD/MIC & CUDA on Stampede Maxim Belkin (Wed Jul 16 2014 - 15:44:34 CDT)
- Re: NAMD/MIC & CUDA on Stampede Maxim Belkin (Thu Jul 17 2014 - 13:32:27 CDT)
Re:Subject: Re: Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Wed Jul 16 2014 - 01:27:52 CDT)
- Re: Subject: Re: Subject: Re:Re: New partial charges after patching Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:53:47 CDT)
- RE: Re:Subject: Re: Subject: Re:Re: New partial charges after patching Tristan Croll (Wed Jul 16 2014 - 18:44:39 CDT)
RE: Force field design Gianluca Interlandi (Wed Jul 16 2014 - 00:32:49 CDT)
- Re: Force field design Sunhwan Jo (Wed Jul 16 2014 - 07:37:19 CDT)
autopsf (patch) Cenk Denktas (Tue Jul 15 2014 - 12:41:48 CDT)
Force field design Abhishek TYAGI (Tue Jul 15 2014 - 11:55:35 CDT)
- Re: Force field design Aron Broom (Tue Jul 15 2014 - 21:58:07 CDT)
  - Re: Force field design Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:06:23 CDT)
  - Re: Force field design Kenno Vanommeslaeghe (Tue Jul 22 2014 - 10:40:37 CDT)
- Re: Force field design Gianluca Interlandi (Tue Jul 15 2014 - 22:32:35 CDT)
- Re: Force field design Mayne, Christopher G (Wed Jul 16 2014 - 10:46:48 CDT)
- Re: Force field design Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:24:29 CDT)
  - RE: Force field design Abhishek TYAGI (Sat Jul 19 2014 - 07:44:53 CDT)
    - Re: Force field design Kenno Vanommeslaeghe (Mon Jul 21 2014 - 10:47:12 CDT)
- RE: Force field design Abhishek TYAGI (Tue Jul 22 2014 - 05:40:00 CDT)
  - Re: Force field design Mayne, Christopher G (Tue Jul 22 2014 - 09:01:58 CDT)
NADH topology file Kevin C Chan (Tue Jul 15 2014 - 05:41:51 CDT)
- Re: NADH topology file Kenno Vanommeslaeghe (Tue Jul 15 2014 - 09:44:10 CDT)
- Re: NADH topology file Kevin C Chan (Wed Jul 16 2014 - 01:51:22 CDT)
  - Re: Re: NADH topology file Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:39:02 CDT)
Fwd: Re: Branko (Mon Jul 14 2014 - 13:24:43 CDT)
(no subject) Eifler, Jay Q. (UMKC-Student) (Mon Jul 14 2014 - 13:05:36 CDT)
- Re: Aron Broom (Mon Jul 14 2014 - 13:18:14 CDT)
- Re: Gianluca Interlandi (Mon Jul 14 2014 - 13:26:57 CDT)
- Re: Kenno Vanommeslaeghe (Mon Jul 14 2014 - 15:58:25 CDT)
Re: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Shailesh Pandey (Fri Jul 11 2014 - 06:14:59 CDT)
AW: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Norman Geist (Fri Jul 11 2014 - 02:51:44 CDT)
Regarding free energy cost incurred by using pseudo bonds Sharmon (Thu Jul 10 2014 - 13:29:29 CDT)
variable force constant Lu Hong (Thu Jul 10 2014 - 12:34:58 CDT)
- Re: variable force constant Aron Broom (Thu Jul 10 2014 - 13:00:32 CDT)
Fwd: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Shailesh Pandey (Thu Jul 10 2014 - 09:31:03 CDT)
Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Shailesh Pandey (Thu Jul 10 2014 - 04:30:20 CDT)
- AW: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Norman Geist (Thu Jul 10 2014 - 05:08:50 CDT)
parameter and topology files for martini polarizable water Klas Karis (Wed Jul 09 2014 - 18:30:23 CDT)
- Re: parameter and topology files for martini polarizable water Fotis Baltoumas (Thu Jul 10 2014 - 04:17:31 CDT)
  - Re: parameter and topology files for martini polarizable water Klas Karis (Thu Jul 10 2014 - 12:11:35 CDT)
accelerated MD as the engine for loop refirement James Starlight (Wed Jul 09 2014 - 14:39:08 CDT)
- Re: accelerated MD as the engine for loop refirement Gianluca Interlandi (Wed Jul 09 2014 - 15:08:17 CDT)
  - Re: accelerated MD as the engine for loop refirement Kenno Vanommeslaeghe (Thu Jul 10 2014 - 17:32:38 CDT)
- Re: accelerated MD as the engine for loop refirement Ajasja LjubetiÄ (Wed Jul 09 2014 - 15:22:15 CDT)
  - Re: accelerated MD as the engine for loop refirement James Starlight (Thu Jul 10 2014 - 04:39:17 CDT)
how to quantify and visualize the flow of water into a protein Thomas Evangelidis (Tue Jul 08 2014 - 18:20:48 CDT)
- Re: how to quantify and visualize the flow of water into a protein Maxim Belkin (Tue Jul 08 2014 - 18:40:15 CDT)
  - Re: how to quantify and visualize the flow of water into a protein Thomas Evangelidis (Tue Jul 08 2014 - 19:04:01 CDT)
- Re: how to quantify and visualize the flow of water into a protein Joshua Adelman (Tue Jul 08 2014 - 19:36:02 CDT)
Bad global crossterm count! Mitul Saha (Tue Jul 08 2014 - 16:46:17 CDT)
- Re: Bad global crossterm count! Mitul Saha (Tue Jul 08 2014 - 16:48:51 CDT)
About asterisk in IC statements in topology files Kevin C Chan (Tue Jul 08 2014 - 02:30:25 CDT)
Hexagonal cell instability during lipid bilayer sim in NAMD 2.9 Michael Bokoch (Mon Jul 07 2014 - 21:42:54 CDT)
NAMD energy plugin - dielectric constant Ramin Ekhteiari (Mon Jul 07 2014 - 14:59:42 CDT)
(no subject) sudipta.mml (Mon Jul 07 2014 - 01:08:12 CDT)
Regarding NAMD and MD simulations Joel Moniz (Mon Jul 07 2014 - 01:42:04 CDT)
- AW: Regarding NAMD and MD simulations Norman Geist (Mon Jul 07 2014 - 02:48:08 CDT)
  - Re: AW: Regarding NAMD and MD simulations Joel Moniz (Tue Jul 08 2014 - 22:17:19 CDT)
two O atoms in CTER are unusually close Fulu Zheng (Sat Jul 05 2014 - 02:05:28 CDT)
- Re: two O atoms in CTER are unusually close Kenno Vanommeslaeghe (Thu Jul 10 2014 - 17:28:08 CDT)
Nanotube tutorial Adam Kells (Fri Jul 04 2014 - 13:19:33 CDT)
(no subject) zmhoseyni (Thu Jul 03 2014 - 22:36:44 CDT)
PMF calculations between membrane and nano particle simulations Subbarao Kanchi (Thu Jul 03 2014 - 15:58:23 CDT)
- Re: PMF calculations between membrane and nano particle simulations Giacomo Fiorin (Thu Jul 03 2014 - 16:34:33 CDT)
  - Re: PMF calculations between membrane and nano particle simulations Subbarao Kanchi (Thu Jul 03 2014 - 17:46:24 CDT)
    - Re: PMF calculations between membrane and nano particle simulations Giacomo Fiorin (Mon Jul 07 2014 - 18:05:06 CDT)
    - Re: PMF calculations between membrane and nano particle simulations Subbarao Kanchi (Tue Jul 08 2014 - 01:01:15 CDT)
Re: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Thu Jul 03 2014 - 04:53:32 CDT)
- AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Thu Jul 03 2014 - 05:38:48 CDT)
- AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Thu Jul 03 2014 - 05:42:02 CDT)
- Re: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Thu Jul 03 2014 - 09:42:41 CDT)
  - Fwd: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Tue Jul 08 2014 - 00:41:54 CDT)
    - AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Tue Jul 08 2014 - 01:12:46 CDT)
- Re: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Tue Jul 08 2014 - 12:14:10 CDT)
  - AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Wed Jul 09 2014 - 02:24:27 CDT)
REMD on IBM iDataPlex DX360M3 Francesco Pietra (Thu Jul 03 2014 - 01:15:21 CDT)
- AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Thu Jul 03 2014 - 04:28:46 CDT)
namd-slurm file Ramin Ekhteiari (Wed Jul 02 2014 - 10:08:31 CDT)
(no subject) zmhoseyni (Wed Jul 02 2014 - 00:25:31 CDT)
Invalid command error Adam Kells (Mon Jun 30 2014 - 06:49:07 CDT)
- Re: Invalid command error Axel Kohlmeyer (Mon Jun 30 2014 - 07:44:41 CDT)
calculating free energy Alireza Mansouri (Sat Jun 28 2014 - 12:22:40 CDT)
- Re: calculating free energy Aron Broom (Sat Jun 28 2014 - 15:53:02 CDT)
Invitation to Submit Review Article Current Protein & Peptide Science (IF: 2.326) Prija Ponnan (Fri Jun 27 2014 - 06:40:43 CDT)
Namd grid forces -distance between molecule and surface Mohan maruthi sena (Fri Jun 27 2014 - 05:20:29 CDT)
Restraints between ion and small molecule Daniel Torrente (Thu Jun 26 2014 - 11:53:49 CDT)
- Re: Restraints between ion and small molecule Kenno Vanommeslaeghe (Thu Jun 26 2014 - 13:16:31 CDT)
Re: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? Shailesh Pandey (Thu Jun 26 2014 - 04:41:49 CDT)
- Re: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? Ivan Gregoretti (Thu Jun 26 2014 - 08:34:16 CDT)
NAMD energy calculation Ramin Ekhteiari (Wed Jun 25 2014 - 11:45:33 CDT)
- Re: vmd-l: NAMD energy calculation John Stone (Mon Jun 30 2014 - 22:59:28 CDT)
  - RE: Re: vmd-l: NAMD energy calculation Morgan, Brittany (Tue Jul 01 2014 - 09:26:44 CDT)
    - Re: Re: vmd-l: NAMD energy calculation Ramin Ekhteiari (Tue Jul 01 2014 - 12:07:47 CDT)
    - RE: Re: vmd-l: NAMD energy calculation Morgan, Brittany (Wed Jul 02 2014 - 11:58:22 CDT)
PMF and work distribution Mustafa Tekpinar (Wed Jun 25 2014 - 05:50:30 CDT)
- Re: PMF and work distribution Giacomo Fiorin (Wed Jun 25 2014 - 12:12:52 CDT)
  - Re: PMF and work distribution Ajasja LjubetiÄ (Thu Jun 26 2014 - 08:05:48 CDT)
Xeon vs i7 and ECC vs SDRAM Gianluca Interlandi (Tue Jun 24 2014 - 20:02:49 CDT)
- Re: Xeon vs i7 and ECC vs SDRAM Gianluca Interlandi (Tue Jun 24 2014 - 23:07:02 CDT)
- AW: Xeon vs i7 and ECC vs SDRAM Norman Geist (Wed Jun 25 2014 - 00:31:47 CDT)
  - Re: AW: Xeon vs i7 and ECC vs SDRAM Gianluca Interlandi (Wed Jun 25 2014 - 01:14:48 CDT)
    - AW: AW: Xeon vs i7 and ECC vs SDRAM Norman Geist (Wed Jun 25 2014 - 01:47:38 CDT)
  - Re: AW: Xeon vs i7 and ECC vs SDRAM Kenno Vanommeslaeghe (Wed Jun 25 2014 - 10:26:26 CDT)
    - AW: AW: Xeon vs i7 and ECC vs SDRAM Norman Geist (Thu Jun 26 2014 - 00:59:13 CDT)
How to apply a magnetic field with NAMD Faezeh Mottaghitalab (Tue Jun 24 2014 - 16:00:48 CDT)
- Re: How to apply a magnetic field with NAMD Ajasja LjubetiÄ (Tue Jun 24 2014 - 16:52:06 CDT)
  - Re: How to apply a magnetic field with NAMD Axel Kohlmeyer (Tue Jun 24 2014 - 19:43:42 CDT)
    - Re: How to apply a magnetic field with NAMD Kenno Vanommeslaeghe (Wed Jun 25 2014 - 10:08:11 CDT)
    - Re: How to apply a magnetic field with NAMD Faezeh Mottaghitalab (Wed Jun 25 2014 - 15:40:43 CDT)
paricle type in residue based coarse graining of NAMD Yongcheng Zhou (Mon Jun 23 2014 - 09:14:12 CDT)
- AW: paricle type in residue based coarse graining of NAMD Norman Geist (Tue Jun 24 2014 - 03:13:21 CDT)
paricle type in residue based coarse graining of NAMD Yongcheng Zhou (Mon Jun 23 2014 - 14:37:16 CDT)
Fatal error.. Gurpreet Kaur Dhindsa (Sun Jun 22 2014 - 17:32:16 CDT)
- AW: Fatal error.. Norman Geist (Mon Jun 23 2014 - 03:33:27 CDT)
memory problem Adam Moser (Fri Jun 20 2014 - 15:01:30 CDT)
NAMD on CRAY XE6m-200: dynamic linking in tcl not working Harish Vashisth (Fri Jun 20 2014 - 14:07:31 CDT)
- Re: NAMD on CRAY XE6m-200: dynamic linking in tcl not working Axel Kohlmeyer (Fri Jun 20 2014 - 14:36:37 CDT)
  - Re: NAMD on CRAY XE6m-200: dynamic linking in tcl not working Harish Vashisth (Fri Jun 20 2014 - 15:17:34 CDT)
  - Re: NAMD on CRAY XE6m-200: dynamic linking in tcl not working Harish Vashisth (Fri Jun 20 2014 - 18:49:59 CDT)
Unsubscribe jafar azamat (Fri Jun 20 2014 - 03:27:10 CDT)
ffTK and phase angles Benjamin Hill (Thu Jun 19 2014 - 17:43:28 CDT)
- Re: ffTK and phase angles Kenno Vanommeslaeghe (Thu Jun 19 2014 - 20:01:05 CDT)
Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Thu Jun 19 2014 - 03:21:33 CDT)
- Re: Subject: Re:Re: New partial charges after patching Kenno Vanommeslaeghe (Thu Jun 19 2014 - 10:11:28 CDT)
  - Re: Subject: Re:Re: New partial charges after patching Kenno Vanommeslaeghe (Fri Jul 11 2014 - 12:19:21 CDT)
Unsubscribe Dhanashree Khanale (Thu Jun 19 2014 - 03:19:51 CDT)
Should PME be used for electrostatic interaction energy calculations? Fotis Baltoumas (Wed Jun 18 2014 - 12:59:16 CDT)
- AW: Should PME be used for electrostatic interaction energy calculations? Norman Geist (Thu Jun 19 2014 - 02:25:49 CDT)
- Re: Should PME be used for electrostatic interaction energy calculations? Thomas Evangelidis (Thu Jun 19 2014 - 02:38:50 CDT)
- AW: Should PME be used for electrostatic interaction energy calculations? Norman Geist (Thu Jun 19 2014 - 02:46:48 CDT)
Constraint failure in RATTLE algorithm Douglas Houston (Wed Jun 18 2014 - 12:29:48 CDT)
- Re: Constraint failure in RATTLE algorithm Axel Kohlmeyer (Wed Jun 18 2014 - 13:23:05 CDT)
  - Re: Constraint failure in RATTLE algorithm Aron Broom (Wed Jun 18 2014 - 14:07:04 CDT)
    - RE: Constraint failure in RATTLE algorithm Tristan Croll (Wed Jun 18 2014 - 20:29:08 CDT)
    - AW: Constraint failure in RATTLE algorithm Norman Geist (Thu Jun 19 2014 - 02:29:16 CDT)
  - Re: Constraint failure in RATTLE algorithm Douglas Houston (Thu Jun 19 2014 - 05:26:53 CDT)
is the aMD implementation compatible with AMBER force fields Thomas Evangelidis (Wed Jun 18 2014 - 06:20:06 CDT)
- Re: is the aMD implementation compatible with AMBER force fields Jeff Wereszczynski (Wed Jun 18 2014 - 13:14:11 CDT)
  - Re: is the aMD implementation compatible with AMBER force fields Thomas Evangelidis (Wed Jun 18 2014 - 18:20:00 CDT)
Inquiry about lipid membrane simulation Mo Chen (Tue Jun 17 2014 - 20:57:59 CDT)
- Re: Inquiry about lipid membrane simulation Kenno Vanommeslaeghe (Wed Jun 18 2014 - 10:20:24 CDT)
  - Re: Inquiry about lipid membrane simulation Kenno Vanommeslaeghe (Wed Jun 18 2014 - 14:02:52 CDT)
Merging the two files...... Gurpreet Kaur Dhindsa (Tue Jun 17 2014 - 10:00:09 CDT)
- Re: Merging the two files...... Aron Broom (Tue Jun 17 2014 - 10:44:36 CDT)
  - Re: Merging the two files...... Aron Broom (Tue Jun 17 2014 - 10:58:22 CDT)
Reg : MD simulation with DMSO instead of water Akshay Bhatnagar (Tue Jun 17 2014 - 06:04:58 CDT)
- Re: Reg : MD simulation with DMSO instead of water Axel Kohlmeyer (Tue Jun 17 2014 - 06:12:55 CDT)
  - Re: Reg : MD simulation with DMSO instead of water Kenno Vanommeslaeghe (Tue Jun 17 2014 - 13:13:02 CDT)
alchemical free energy simulations with parmtop Hannes Loeffler (Tue Jun 17 2014 - 04:35:59 CDT)
- Re: alchemical free energy simulations with parmtop Hannes Loeffler (Mon Dec 01 2014 - 03:20:17 CST)
  - Re: Re: alchemical free energy simulations with parmtop Jim Phillips (Tue Dec 02 2014 - 12:06:40 CST)
improving tclforce efficiency, getting "Signal: segmentation violation" error zeynab mohamad hoseyni (Sun Jun 15 2014 - 20:18:11 CDT)
unsubscribe Laura (Sun Jun 15 2014 - 12:29:39 CDT)
The short range nonbonbed force charge after load balancing Â¬Óíï¿ (Sun Jun 15 2014 - 04:57:43 CDT)
New partial charges after patching Sadegh Faramarzi Ganjabad (Sat Jun 14 2014 - 04:15:47 CDT)
- Re: New partial charges after patching Kenno Vanommeslaeghe (Mon Jun 16 2014 - 10:23:02 CDT)
About converting NAMD dcd file into CHARMM dcd file Mo Chen (Fri Jun 13 2014 - 18:41:30 CDT)
- Re: About converting NAMD dcd file into CHARMM dcd file Kenno Vanommeslaeghe (Fri Jun 13 2014 - 21:18:52 CDT)
Re: AW: Using nodelist file causes namd to hang Douglas Houston (Fri Jun 13 2014 - 12:17:15 CDT)
- AW: AW: Using nodelist file causes namd to hang Norman Geist (Mon Jun 16 2014 - 02:19:28 CDT)
  - Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Wed Jun 18 2014 - 07:24:00 CDT)
AW: Reg: movement of protein outside box Norman Geist (Fri Jun 13 2014 - 03:09:20 CDT)
How to refer to side-chain via tcl-force scripting? zeynab mohamad hoseyni (Fri Jun 13 2014 - 00:53:12 CDT)
- RE: How to refer to side-chain via tcl-force scripting? Tristan Croll (Fri Jun 13 2014 - 02:08:51 CDT)
- AW: How to refer to side-chain via tcl-force scripting? Norman Geist (Fri Jun 13 2014 - 02:53:41 CDT)
- AW: How to refer to side-chain via tcl-force scripting? Norman Geist (Fri Jun 13 2014 - 02:56:03 CDT)
  - Re: AW: How to refer to side-chain via tcl-force scripting? zeynab mohamad hoseyni (Fri Jun 13 2014 - 03:21:08 CDT)
NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults Vlastimil ZÃma (Wed Jun 11 2014 - 02:36:44 CDT)
- Re: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults Axel Kohlmeyer (Wed Jun 11 2014 - 02:42:48 CDT)
  - Re: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults Axel Kohlmeyer (Wed Jun 11 2014 - 03:13:56 CDT)
- AW: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults Norman Geist (Wed Jun 11 2014 - 03:07:21 CDT)
AW: Reg: movement of protein outside box Norman Geist (Tue Jun 10 2014 - 07:26:58 CDT)
Reg: movement of protein outside box Akshay Bhatnagar (Mon Jun 09 2014 - 20:46:56 CDT)
- Re: Reg: movement of protein outside box Aron Broom (Mon Jun 09 2014 - 22:09:28 CDT)
- AW: Reg: movement of protein outside box Norman Geist (Tue Jun 10 2014 - 02:47:32 CDT)
NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? Shailesh Pandey (Mon Jun 09 2014 - 12:54:03 CDT)
- AW: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? Norman Geist (Tue Jun 10 2014 - 02:43:11 CDT)
boron nitride nanotube Z (Mon Jun 09 2014 - 02:58:02 CDT)
- Re: boron nitride nanotube Axel Kohlmeyer (Mon Jun 09 2014 - 04:19:24 CDT)
  - Re: boron nitride nanotube Z (Thu Jun 12 2014 - 05:28:33 CDT)
    - Re: boron nitride nanotube Axel Kohlmeyer (Thu Jun 12 2014 - 05:46:33 CDT)
change in pdb.. Gurpreet Kaur Dhindsa (Sat Jun 07 2014 - 18:37:41 CDT)
- change in pdb.. Gurpreet Kaur Dhindsa (Wed Jun 11 2014 - 09:39:31 CDT)
  - Re: change in pdb.. Ivan Gregoretti (Wed Jun 11 2014 - 10:29:05 CDT)
NAMD Multicore CUDA usage Ravi Abrol (Fri Jun 06 2014 - 14:20:10 CDT)
- AW: NAMD Multicore CUDA usage Norman Geist (Tue Jun 10 2014 - 02:33:13 CDT)
alchElecLambdaStart (Thermodynamic Integration) Javad Noroozi (Fri Jun 06 2014 - 13:55:28 CDT)
Reg: deformation of water box during equilibration Akshay Bhatnagar (Fri Jun 06 2014 - 11:35:34 CDT)
- Re: Reg: deformation of water box during equilibration Aron Broom (Fri Jun 06 2014 - 12:37:30 CDT)
  - Re: Reg: deformation of water box during equilibration Akshay Bhatnagar (Fri Jun 06 2014 - 21:15:30 CDT)
Fixed atoms. Gurpreet Kaur Dhindsa (Thu Jun 05 2014 - 16:15:05 CDT)
- Re: Fixed atoms. Aron Broom (Thu Jun 05 2014 - 17:03:12 CDT)
  - Re: Fixed atoms. Maxim Belkin (Thu Jun 05 2014 - 17:14:48 CDT)
NAMD energy plugin Ramin Ekhteiari (Wed Jun 04 2014 - 12:45:36 CDT)
- Re: NAMD energy plugin Aron Broom (Wed Jun 04 2014 - 13:34:51 CDT)
  - Re: NAMD energy plugin Ramin Ekhteiari (Wed Jun 04 2014 - 13:55:23 CDT)
    - Re: NAMD energy plugin Kenno Vanommeslaeghe (Wed Jun 04 2014 - 14:16:48 CDT)
  - Re: NAMD energy plugin Kenno Vanommeslaeghe (Wed Jun 04 2014 - 14:10:39 CDT)
    - Re: NAMD energy plugin MEHRAN MB (Wed Jun 04 2014 - 15:16:09 CDT)
non-neutralized system Research Jubilant (Wed Jun 04 2014 - 10:29:47 CDT)
Ion Au+3 simulation Daniel Torrente (Tue Jun 03 2014 - 13:31:40 CDT)
- Re: Ion Au+3 simulation Axel Kohlmeyer (Tue Jun 03 2014 - 14:38:35 CDT)
  - Re: Ion Au+3 simulation Daniel Torrente (Tue Jun 03 2014 - 15:17:15 CDT)
Density of water box Akshay Bhatnagar (Tue Jun 03 2014 - 05:22:00 CDT)
- Re: Density of water box Ana Celia Vila Verde (Tue Jun 03 2014 - 06:29:02 CDT)
  - Re: Density of water box Akshay Bhatnagar (Tue Jun 03 2014 - 07:26:41 CDT)
coordinates in namd Research Jubilant (Mon Jun 02 2014 - 23:34:52 CDT)
- AW: coordinates in namd Norman Geist (Tue Jun 03 2014 - 01:40:14 CDT)
- RE: coordinates in namd Tristan Croll (Tue Jun 03 2014 - 02:25:49 CDT)
About electrostatic treatment Mo Chen (Fri May 30 2014 - 19:35:50 CDT)
- Re: About electrostatic treatment Mo Chen (Fri May 30 2014 - 19:39:31 CDT)
- Re: About electrostatic treatment David Hardy (Sat May 31 2014 - 12:01:34 CDT)
code implementation based on NAMD source code Teerapong Pirojsirikul (Thu May 29 2014 - 17:39:21 CDT)
FEP of water molecule in binding pocket Monika Sharma (Wed May 28 2014 - 15:35:33 CDT)
Rapid and accurate parameterization of new molecules in CHARMM Aaron Larsen (Tue May 27 2014 - 08:21:06 CDT)
- RE: Rapid and accurate parameterization of new molecules in CHARMM JC Gumbart (Tue May 27 2014 - 09:19:40 CDT)
  - RE: Rapid and accurate parameterization of new molecules in CHARMM Tristan Croll (Tue May 27 2014 - 17:23:07 CDT)
  - Re: Rapid and accurate parameterization of new molecules in CHARMM Kenno Vanommeslaeghe (Tue May 27 2014 - 17:58:42 CDT)
    - Re: Rapid and accurate parameterization of new molecules in CHARMM Aaron Larsen (Tue May 27 2014 - 19:22:22 CDT)
    - Re: Rapid and accurate parameterization of new molecules in CHARMM Kenno Vanommeslaeghe (Wed May 28 2014 - 10:35:07 CDT)
constraint file from amber prmtop/inpcrd amin_at_imtech.res.in (Sat May 24 2014 - 14:32:55 CDT)
IMPROPER PARAMETERS FOR CA CA CA CA Z (Sat May 24 2014 - 10:50:49 CDT)
- Re: IMPROPER PARAMETERS FOR CA CA CA CA Kenno Vanommeslaeghe (Mon May 26 2014 - 16:42:29 CDT)
  - Re: IMPROPER PARAMETERS FOR CA CA CA CA Axel Kohlmeyer (Mon May 26 2014 - 16:47:44 CDT)
*** glibc detected *** namd2: invalid fastbin entry (free) Wesley Lay (Thu May 22 2014 - 15:19:11 CDT)
(no subject) zmhoseyni (Wed May 21 2014 - 04:48:25 CDT)
building namd on a Cray XE6 with Interlagos procs Giovanni Settanni (Tue May 20 2014 - 09:03:22 CDT)
(no subject) zmhoseyni (Mon May 19 2014 - 04:18:48 CDT)
COLVAR metadynamics: center of mass of atoms crossing simulation box Lorenz Ripka (Mon May 19 2014 - 03:44:36 CDT)
- COLVAR metadynamics: center of mass of atoms crossing simulation box Lorenz Ripka (Mon May 19 2014 - 07:17:47 CDT)
  - Re: COLVAR metadynamics: center of mass of atoms crossing simulation box Giacomo Fiorin (Tue May 20 2014 - 11:41:56 CDT)
    - Re: COLVAR metadynamics: center of mass of atoms crossing simulation box Lorenz Ripka (Fri May 23 2014 - 07:35:23 CDT)
Re: Steered MD with the RMSD colvar George Patargias (Mon May 19 2014 - 05:01:12 CDT)
- Re: Steered MD with the RMSD colvar Giacomo Fiorin (Wed May 21 2014 - 17:52:54 CDT)
  - Re: Steered MD with the RMSD colvar George Patargias (Thu Jul 03 2014 - 06:26:19 CDT)
Workshop on Very Large System Simulation Workshop, Urbana, IL, August 11-15, 2014 David Brandon (Sat May 17 2014 - 18:22:07 CDT)
running Multiple-replicas metadynamics Osvalds Verners (Fri May 16 2014 - 13:01:08 CDT)
- Re: running Multiple-replicas metadynamics Giacomo Fiorin (Fri May 16 2014 - 14:00:41 CDT)
  - Re: running Multiple-replicas metadynamics Osvalds Verners (Fri May 16 2014 - 14:21:28 CDT)
Polymer Layer/ Cutoff Rawan Al Nsour (Thu May 15 2014 - 11:19:21 CDT)
- Re: Polymer Layer/ Cutoff Kenno Vanommeslaeghe (Thu May 15 2014 - 11:58:43 CDT)
  - Re: Polymer Layer/ Cutoff Kenno Vanommeslaeghe (Thu May 15 2014 - 14:34:00 CDT)
    - Re: Polymer Layer/ Cutoff Rawan Al Nsour (Thu May 15 2014 - 16:13:58 CDT)
    - Re: Polymer Layer/ Cutoff Kenno Vanommeslaeghe (Thu May 15 2014 - 18:00:42 CDT)
NAMD-GPU Ramin Ekhteiari (Wed May 14 2014 - 07:19:10 CDT)
- Re: NAMD-GPU Axel Kohlmeyer (Wed May 14 2014 - 07:51:37 CDT)
  - Re: NAMD-GPU Aron Broom (Wed May 14 2014 - 09:54:20 CDT)
Scaling solvent-solute intermolecular interactions Michael Bellucci (Tue May 13 2014 - 13:34:13 CDT)
- Re: Scaling solvent-solute intermolecular interactions Axel Kohlmeyer (Tue May 13 2014 - 13:56:02 CDT)
  - RE: Scaling solvent-solute intermolecular interactions Michael Bellucci (Tue May 13 2014 - 15:09:06 CDT)
NAMD-SMP-Ibverbs-CUDA assistance Matthew Ralph Adendorff (Tue May 13 2014 - 09:25:44 CDT)
- AW: NAMD-SMP-Ibverbs-CUDA assistance Norman Geist (Wed May 14 2014 - 00:42:51 CDT)
Dual boost accelerated md energy parameters? Per Larsson (Mon May 12 2014 - 13:54:48 CDT)
- Re: Dual boost accelerated md energy parameters? Thomas Evangelidis (Mon May 12 2014 - 14:11:45 CDT)
unsubscribe Shalton Evans (Sun May 11 2014 - 19:18:39 CDT)
Protein solvation farzad kiani (Sat May 10 2014 - 12:28:26 CDT)
- Re: Protein solvation Kipp Johnson (Sat May 10 2014 - 15:38:26 CDT)
FixedAtoms and Reference group in spinangle colvar nicolas martin (Fri May 09 2014 - 09:01:28 CDT)
- Re: FixedAtoms and Reference group in spinangle colvar JÃ©rÃ´me HÃ©nin (Fri May 09 2014 - 13:53:56 CDT)
  - Re: FixedAtoms and Reference group in spinangle colvar nicolas martin (Sun May 11 2014 - 16:52:42 CDT)
error while making psf file for bacteriorhodopsin system Faezeh Mottaghitalab (Thu May 08 2014 - 15:11:26 CDT)
- Re: error while making psf file for bacteriorhodopsin system Kenno Vanommeslaeghe (Thu May 08 2014 - 15:57:52 CDT)
  - Re: error while making psf file for bacteriorhodopsin system Kenno Vanommeslaeghe (Fri May 09 2014 - 11:38:08 CDT)
    - Re: error while making psf file for bacteriorhodopsin system Faezeh Mottaghitalab (Fri May 09 2014 - 13:10:55 CDT)
PMF from ABF simulation not plateauing Riley Workman (Thu May 08 2014 - 12:08:13 CDT)
- Re: PMF from ABF simulation not plateauing Aron Broom (Thu May 08 2014 - 13:56:37 CDT)
- Re: PMF from ABF simulation not plateauing JÃ©rÃ´me HÃ©nin (Thu May 08 2014 - 17:37:20 CDT)
Setting up membrane protein simulation from existing conformation? Per Larsson (Wed May 07 2014 - 14:17:41 CDT)
- Re: Setting up membrane protein simulation from existing conformation? Kenno Vanommeslaeghe (Wed May 07 2014 - 14:44:00 CDT)
  - Re: Setting up membrane protein simulation from existing conformation? Per Larsson (Wed May 07 2014 - 15:12:53 CDT)
NAMD and NUMA Joseph Farran (Wed May 07 2014 - 13:54:51 CDT)
- AW: NAMD and NUMA Norman Geist (Thu May 08 2014 - 01:53:12 CDT)
  - Re: AW: NAMD and NUMA Joseph Farran (Thu May 08 2014 - 11:28:46 CDT)
  - Re: AW: NAMD and NUMA Joseph Farran (Thu May 08 2014 - 11:33:25 CDT)
choose the best equilibrium arrangement of water molecules Boshra Moradi (Tue May 06 2014 - 16:55:17 CDT)
(no subject) Boshra Moradi (Tue May 06 2014 - 16:35:44 CDT)
TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed Norman Geist (Tue May 06 2014 - 05:49:45 CDT)
- Re: TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed Maxim Belkin (Wed May 07 2014 - 16:15:22 CDT)
  - AW: TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed Norman Geist (Thu May 08 2014 - 01:54:10 CDT)
Topology for lysine bouding in Epsilon Jean-Patrick Francoia (Mon May 05 2014 - 12:11:23 CDT)
- Re: Topology for lysine bouding in Epsilon Kenno Vanommeslaeghe (Mon May 05 2014 - 15:07:31 CDT)
  - Re: Topology for lysine bouding in Epsilon Kenno Vanommeslaeghe (Tue May 06 2014 - 13:06:38 CDT)
Colvars keyword problem Sofya Lushchekina (Mon May 05 2014 - 09:32:11 CDT)
- Re: Colvars keyword problem JÃ©rÃ´me HÃ©nin (Mon May 05 2014 - 10:01:03 CDT)
Empirical force fields: release new version of RED Server Dev/PyRED FyD (Mon May 05 2014 - 06:07:18 CDT)
Force field for sulfated tyrosines Shaon Chakrabarti (Sun May 04 2014 - 21:35:38 CDT)
- Re: Force field for sulfated tyrosines Kenno Vanommeslaeghe (Mon May 05 2014 - 13:11:47 CDT)
Patch to connect monomers code Rawan Al Nsour (Sun May 04 2014 - 12:15:12 CDT)
- Re: Patch to connect monomers code Kenno Vanommeslaeghe (Mon May 05 2014 - 13:11:36 CDT)
  - Re: Patch to connect monomers code Kenno Vanommeslaeghe (Tue May 06 2014 - 13:33:49 CDT)
Getting extra atoms by Patching! Sadegh Faramarzi Ganjabad (Fri May 02 2014 - 18:51:31 CDT)
- Re: Getting extra atoms by Patching! Michelle Kuttel (Sat May 03 2014 - 01:11:50 CDT)
  - Re: Getting extra atoms by Patching! Kenno Vanommeslaeghe (Mon May 05 2014 - 11:45:48 CDT)
  - Re: Getting extra atoms by Patching! Kenno Vanommeslaeghe (Thu May 08 2014 - 12:38:10 CDT)
    - Fwd: Getting extra atoms by Patching! Sadegh Faramarzi Ganjabad (Thu May 08 2014 - 15:49:14 CDT)
Re: Teflon New Residue Rawan Al Nsour (Fri May 02 2014 - 11:10:38 CDT)
- Re: Teflon New Residue Kenno Vanommeslaeghe (Fri May 02 2014 - 12:21:09 CDT)
Teflon New Residue Rawan Al Nsour (Fri May 02 2014 - 09:57:57 CDT)
How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory zeynab mohamad hoseyni (Mon Apr 28 2014 - 23:12:57 CDT)
- AW: How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory Norman Geist (Tue Apr 29 2014 - 02:20:33 CDT)
- AW: How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory Norman Geist (Tue Apr 29 2014 - 02:21:20 CDT)
FEP is in kj/mol Javad Noroozi (Sun Apr 27 2014 - 08:32:33 CDT)
Using the CHARMM36 forcefield with NAMD Alex Utev (CMP) (Wed Apr 23 2014 - 11:15:08 CDT)
- Re: Using the CHARMM36 forcefield with NAMD Kenno Vanommeslaeghe (Wed Apr 23 2014 - 12:28:33 CDT)
  - Re: Using the CHARMM36 forcefield with NAMD Kenno Vanommeslaeghe (Fri May 09 2014 - 11:50:45 CDT)
FATAL ERROR: Setting parameter tclForces from script failed! zeynab mohamad hoseyni (Tue Apr 22 2014 - 02:43:23 CDT)
TI analysis script Javad Noroozi (Sat Apr 19 2014 - 08:16:18 CDT)
Workshop on GPU Programming for Molecular Modeling, in Urbana, Illinois, July 22-24, 2014 David Brandon (Fri Apr 18 2014 - 16:49:02 CDT)
Collective Variables to Restrain Ions Away From Protein Chris Ing (Thu Apr 17 2014 - 18:36:06 CDT)
- Re: Collective Variables to Restrain Ions Away From Protein Aron Broom (Thu Apr 17 2014 - 23:15:35 CDT)
  - Re: Collective Variables to Restrain Ions Away From Protein Aron Broom (Sun Apr 20 2014 - 00:27:37 CDT)
peptide tends to migrate out the water box Francesco Pietra (Thu Apr 17 2014 - 17:02:01 CDT)
- Re: peptide tends to migrate out the water box Ana Celia Vila Verde (Fri Apr 18 2014 - 02:12:40 CDT)
  - Re: peptide tends to migrate out the water box Francesco Pietra (Fri Apr 18 2014 - 03:14:49 CDT)
- Re: peptide tends to migrate out the water box Kenno Vanommeslaeghe (Fri Apr 18 2014 - 10:27:09 CDT)
CUDA error in cuda_check_local_progress Abhishek TYAGI (Thu Apr 17 2014 - 02:41:11 CDT)
- AW: CUDA error in cuda_check_local_progress Norman Geist (Thu Apr 17 2014 - 03:21:44 CDT)
  - RE: CUDA error in cuda_check_local_progress Abhishek TYAGI (Thu Apr 17 2014 - 04:07:36 CDT)
  - RE: CUDA error in cuda_check_local_progress Abhishek TYAGI (Thu Apr 17 2014 - 04:23:44 CDT)
    - AW: CUDA error in cuda_check_local_progress Norman Geist (Thu Apr 17 2014 - 04:50:10 CDT)
    - AW: CUDA error in cuda_check_local_progress Norman Geist (Tue Apr 22 2014 - 00:39:49 CDT)
How to setup a system with two pulling directions John Xi (Wed Apr 16 2014 - 19:32:27 CDT)
- Re: How to setup a system with two pulling directions Felipe Merino (Thu Apr 17 2014 - 10:38:06 CDT)
  - Re: How to setup a system with two pulling directions John Xi (Thu Apr 17 2014 - 19:48:39 CDT)
RBCG and NAMD 2.9 Raul Araya (Wed Apr 16 2014 - 13:21:43 CDT)
- Re: RBCG and NAMD 2.9 Ramya Gamini (Wed Apr 16 2014 - 14:49:54 CDT)
Step size in FEP calculation Javad Noroozi (Tue Apr 15 2014 - 23:21:35 CDT)
NAMD-Lite Hassan Kianinejad (Tue Apr 15 2014 - 17:22:56 CDT)
- Re: NAMD-Lite Axel Kohlmeyer (Tue Apr 15 2014 - 17:42:32 CDT)
  - Re: NAMD-Lite Axel Kohlmeyer (Tue Apr 15 2014 - 18:22:54 CDT)
- Re: NAMD-Lite Gianluca Interlandi (Tue Apr 15 2014 - 18:16:50 CDT)
Altering extrabonds forces during MD Bryan Roessler (Tue Apr 15 2014 - 09:53:02 CDT)
ABF with the RMSD colvar George Patargias (Tue Apr 15 2014 - 05:22:46 CDT)
- Re: ABF with the RMSD colvar Giacomo Fiorin (Tue Apr 15 2014 - 10:06:44 CDT)
(no subject) manish kesherwani (Tue Apr 15 2014 - 00:02:12 CDT)
- Re: Kenno Vanommeslaeghe (Tue Apr 15 2014 - 12:14:07 CDT)
  - Re: Aron Broom (Tue Apr 15 2014 - 13:47:48 CDT)
    - Re: manish kesherwani (Wed Apr 16 2014 - 13:21:34 CDT)
full electrostatics and pairlistdist Jonathan Phillips (Mon Apr 14 2014 - 16:25:04 CDT)
- Re: full electrostatics and pairlistdist Jason Swails (Wed Apr 16 2014 - 08:27:34 CDT)
  - Re: full electrostatics and pairlistdist Jonathan Phillips (Fri Apr 18 2014 - 05:51:02 CDT)
FEP error using CUDA Sadegh Faramarzi Ganjabad (Sun Apr 13 2014 - 22:42:12 CDT)
- Re: FEP error using CUDA Gianluca Interlandi (Sun Apr 13 2014 - 23:14:03 CDT)
Simulation crash during NPT equilibration James Starlight (Fri Apr 11 2014 - 05:58:17 CDT)
- AW: Simulation crash during NPT equilibration Norman Geist (Fri Apr 11 2014 - 06:31:49 CDT)
Nanotube Simulation Miro Hodak (Thu Apr 10 2014 - 18:02:56 CDT)
- Re: Nanotube Simulation Axel Kohlmeyer (Fri Apr 11 2014 - 03:36:44 CDT)
  - Re: Nanotube Simulation Miro Hodak (Fri Apr 11 2014 - 11:56:59 CDT)
Accelerated MD with transmembrane protein Kevin Kastner (Thu Apr 10 2014 - 13:40:26 CDT)
- Re: Accelerated MD with transmembrane protein Felipe Merino (Fri Apr 11 2014 - 03:27:09 CDT)
  - Re: Accelerated MD with transmembrane protein Jeff Wereszczynski (Fri Apr 11 2014 - 07:19:20 CDT)
Collective variable module naresh kumar (Thu Apr 10 2014 - 11:36:07 CDT)
- Re: Collective variable module Giacomo Fiorin (Thu Apr 10 2014 - 12:03:27 CDT)
  - Re: Collective variable module naresh kumar (Thu Apr 10 2014 - 12:54:02 CDT)
unsuscribe Cat Chenal (Thu Apr 10 2014 - 09:49:18 CDT)
MMPBSA Energy Calculations using VMD (Post-Processing) Aditya Ranganathan (Thu Apr 10 2014 - 08:25:41 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) Fotis Baltoumas (Thu Apr 10 2014 - 10:09:00 CDT)
  - Re: MMPBSA Energy Calculations using VMD (Post-Processing) James Starlight (Sat Apr 12 2014 - 01:53:35 CDT)
RE: slice of water box Hongbo Du (Wed Apr 09 2014 - 20:22:04 CDT)
- AW: slice of water box Norman Geist (Thu Apr 10 2014 - 01:46:05 CDT)
slice of water box Boshra Moradi (Wed Apr 09 2014 - 17:13:12 CDT)
Problems with energy minimization James Starlight (Wed Apr 09 2014 - 09:07:28 CDT)
- Re: Problems with energy minimization Subbarao Kanchi (Wed Apr 09 2014 - 09:14:55 CDT)
  - Re: Problems with energy minimization James Starlight (Wed Apr 09 2014 - 09:38:21 CDT)
AW: AW: Using nodelist file causes namd to hang Norman Geist (Wed Apr 09 2014 - 05:53:50 CDT)
- Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Wed Apr 09 2014 - 06:16:35 CDT)
  - AW: AW: AW: Using nodelist file causes namd to hang Norman Geist (Wed Apr 09 2014 - 07:09:53 CDT)
- Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Mon Jun 02 2014 - 04:50:40 CDT)
PMETolerance Natalie Esther Smith (Tue Apr 08 2014 - 23:07:52 CDT)
posting from Yahoo addresses disabled Jim Phillips (Tue Apr 08 2014 - 17:45:15 CDT)
Point group symmetry bmaiti_at_andrew.cmu.edu (Mon Apr 07 2014 - 18:20:08 CDT)
the dielectric constant use in pairwise interaction energy calculation of ligand and protein Patrick Chiu (Tue Apr 08 2014 - 08:45:11 CDT)
- RE: the dielectric constant use in pairwise interaction energy calculation of ligand and protein Hongbo Du (Tue Apr 08 2014 - 10:01:01 CDT)
Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Mon Apr 07 2014 - 11:33:50 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Wed Apr 09 2014 - 10:41:35 CDT)
Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Mon Apr 07 2014 - 11:33:58 CDT)
Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Mon Apr 07 2014 - 11:32:49 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! Giacomo Fiorin (Mon Apr 07 2014 - 19:54:30 CDT)
  - Re: Spinangle with refgroup : Warning: discontinuous rotation! Giacomo Fiorin (Wed Apr 09 2014 - 11:18:13 CDT)
  - Re: Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Thu Apr 10 2014 - 09:04:21 CDT)
Electronic density profile of lipid bilayer. Subbarao Kanchi (Sun Apr 06 2014 - 20:32:54 CDT)
Movie of a channel trajectory Javier Cáceres Delpiano (Sat Apr 05 2014 - 22:26:21 CDT)
- AW: Movie of a channel trajectory Norman Geist (Mon Apr 07 2014 - 02:05:25 CDT)
medwater config Hassan Kianinejad (Fri Apr 04 2014 - 19:15:32 CDT)
SHAKE or RATTLE algorithm Ramin Ekhteiari (Fri Apr 04 2014 - 15:08:04 CDT)
- Re: SHAKE or RATTLE algorithm Axel Kohlmeyer (Fri Apr 04 2014 - 15:44:45 CDT)
  - Re: SHAKE or RATTLE algorithm David Hardy (Fri Apr 04 2014 - 16:28:54 CDT)
Re: residue_rmsd.tcl segmentation fault Axel Kohlmeyer (Fri Apr 04 2014 - 03:03:55 CDT)
- AW: residue_rmsd.tcl segmentation fault Norman Geist (Fri Apr 04 2014 - 03:18:08 CDT)
- Re: residue_rmsd.tcl segmentation fault Axel Kohlmeyer (Fri Apr 04 2014 - 04:12:38 CDT)
residue_rmsd.tcl segmentation fault John Xi (Thu Apr 03 2014 - 21:49:05 CDT)
- AW: residue_rmsd.tcl segmentation fault Norman Geist (Fri Apr 04 2014 - 02:53:45 CDT)
  - Re: AW: residue_rmsd.tcl segmentation fault John Xi (Fri Apr 04 2014 - 07:04:45 CDT)
"Hands-on" Workshop on Computational Biophysics at Lake Tahoe, August 4-8, 2014 David Brandon (Thu Apr 03 2014 - 11:17:33 CDT)
Using position-dependent diffusion to simulate long colvars trajectories Ajasja LjubetiÄ (Thu Apr 03 2014 - 07:36:28 CDT)
6 equilibration steps at charmm gui server Ramin Ekhteiari (Thu Apr 03 2014 - 04:32:58 CDT)
- Re: 6 equilibration steps at charmm gui server Sunhwan Jo (Thu Apr 03 2014 - 09:34:23 CDT)
NAMD Pressure profile calculations Tao Qu (Wed Apr 02 2014 - 15:43:59 CDT)
Multiple dihedral with multiplicity of 7 greater than max of 6 Rawan Al Nsour (Wed Apr 02 2014 - 13:44:33 CDT)
Multiple dihedral with multiplicity of 7 greater than max of 6 Rawan Al Nsour (Wed Apr 02 2014 - 13:38:53 CDT)
- Re: Multiple dihedral with multiplicity of 7 greater than max of 6 Axel Kohlmeyer (Wed Apr 02 2014 - 13:52:18 CDT)
- Re: Multiple dihedral with multiplicity of 7 greater than max of 6 Kenno Vanommeslaeghe (Wed Apr 02 2014 - 14:05:49 CDT)
Excluding non bonded interactions between segments Fotis Baltoumas (Wed Apr 02 2014 - 07:40:29 CDT)
- Re: Excluding non bonded interactions between segments JÃ©rÃ´me HÃ©nin (Wed Apr 02 2014 - 08:09:21 CDT)
  - Re: Excluding non bonded interactions between segments Fotis Baltoumas (Tue Apr 08 2014 - 06:57:35 CDT)
    - Re: Excluding non bonded interactions between segments JÃ©rÃ´me HÃ©nin (Tue Apr 08 2014 - 06:56:22 CDT)
    - Re: Excluding non bonded interactions between segments Fotis Baltoumas (Tue Apr 08 2014 - 07:08:40 CDT)
Re: Assigning different temperatures to simulation Jhonatam Cordeiro Rodrigues (Wed Apr 02 2014 - 00:42:17 CDT)
- Re: Assigning different temperatures to simulation JÃ©rÃ´me HÃ©nin (Wed Apr 02 2014 - 02:35:40 CDT)
  - AW: Assigning different temperatures to simulation Norman Geist (Wed Apr 02 2014 - 02:45:57 CDT)
  - Re: Assigning different temperatures to simulation JÃ©rÃ´me HÃ©nin (Wed Apr 02 2014 - 03:16:30 CDT)
    - Re: Assigning different temperatures to simulation Jhonatam Cordeiro Rodrigues (Thu Apr 03 2014 - 15:24:09 CDT)
Random segfault for MPI based REMD at startup Norman Geist (Wed Apr 02 2014 - 00:34:20 CDT)
Assigning different temperatures to simulation Jhonatam Cordeiro Rodrigues (Tue Apr 01 2014 - 15:29:36 CDT)
- AW: Assigning different temperatures to simulation Norman Geist (Wed Apr 02 2014 - 00:02:58 CDT)
- AW: Assigning different temperatures to simulation Norman Geist (Wed Apr 02 2014 - 00:06:08 CDT)
question Eifler, Jay Q. (UMKC-Student) (Mon Mar 31 2014 - 11:47:16 CDT)
- Re: question JÃ©rÃ´me HÃ©nin (Mon Mar 31 2014 - 12:26:01 CDT)
accelerated MD log Felipe Merino (Mon Mar 31 2014 - 03:57:30 CDT)
Re: remd across gpus Francesco Pietra (Mon Mar 31 2014 - 02:41:24 CDT)
- AW: remd across gpus Norman Geist (Mon Mar 31 2014 - 04:13:21 CDT)
Constraint failure in RATTLE Francesco Pietra (Sun Mar 30 2014 - 02:31:54 CDT)
- Fwd: Constraint failure in RATTLE Francesco Pietra (Sun Mar 30 2014 - 03:07:50 CDT)
- Re: Constraint failure in RATTLE Massimiliano Porrini (Sun Mar 30 2014 - 06:49:34 CDT)
accelMD on GPUs Francesco Pietra (Sat Mar 29 2014 - 02:38:58 CDT)
remd across gpus Francesco Pietra (Sat Mar 29 2014 - 02:29:12 CDT)
- AW: remd across gpus Norman Geist (Mon Mar 31 2014 - 00:39:03 CDT)
Help to solve the error Flora Chettiar (Wed Mar 26 2014 - 04:00:46 CDT)
- Re: Help to solve the error Ivan Gregoretti (Wed Mar 26 2014 - 17:11:58 CDT)
  - Re: Help to solve the error Flora Chettiar (Thu Mar 27 2014 - 01:47:09 CDT)
    - Re: Help to solve the error Ivan Gregoretti (Thu Mar 27 2014 - 07:20:50 CDT)
hey! you! why did my simulation crash? Edward Lyman (Wed Mar 26 2014 - 10:42:46 CDT)
Question about accelerated MD Mare Libero (Tue Mar 25 2014 - 17:14:27 CDT)
- AW: Question about accelerated MD Norman Geist (Wed Mar 26 2014 - 02:34:20 CDT)
  - Re: AW: Question about accelerated MD Mare Libero (Wed Mar 26 2014 - 10:12:13 CDT)
Compiling with Open64 4.5.2.1 for AMD Opteron 6378 David Chin (Mon Mar 24 2014 - 10:44:54 CDT)
coarse-grained simulation: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C5M P5 (ATOMS 1 2) Khaled Barakat (Sun Mar 23 2014 - 22:44:02 CDT)
PME: The Excluded Coulombic Interactions Hadi (Fri Mar 21 2014 - 22:56:50 CDT)
wrapping option in namd Research Jubilant (Wed Mar 19 2014 - 21:34:57 CDT)
- Re: wrapping option in namd Ivan Gregoretti (Wed Mar 19 2014 - 21:58:30 CDT)
  - Re: vmd-l: Re: wrapping option in namd Research Jubilant (Wed Mar 19 2014 - 22:38:16 CDT)
    - Re: vmd-l: Re: wrapping option in namd MEHRAN MB (Tue Apr 01 2014 - 21:44:36 CDT)
  - Fwd: vmd-l: Re: wrapping option in namd Christian Jorgensen (Mon Jun 23 2014 - 04:59:50 CDT)
Re: Restoring simulation from the previous run James Starlight (Wed Mar 19 2014 - 09:38:18 CDT)
Restoring simulation from the previous run James Starlight (Wed Mar 19 2014 - 03:32:31 CDT)
Improve scaling for large amount of fixed atoms Norman Geist (Wed Mar 19 2014 - 03:19:38 CDT)
- Re: Improve scaling for large amount of fixed atoms Tristan Croll (Wed Mar 19 2014 - 21:15:40 CDT)
changing damping coefficient during simulation Gozde Eskici (Tue Mar 18 2014 - 10:20:25 CDT)
iDataPlex Francesco Pietra (Mon Mar 17 2014 - 13:12:32 CDT)
- Re: iDataPlex Andrew Emerson (Tue Mar 18 2014 - 03:15:30 CDT)
  - Re: iDataPlex Francesco Pietra (Tue Mar 18 2014 - 04:03:29 CDT)
Detection of Internal water along MD trajectory James Starlight (Mon Mar 17 2014 - 04:14:38 CDT)
Free Energy Calculation Using Thermodynamic Integration Javad Noroozi (Mon Mar 17 2014 - 02:06:08 CDT)
TCL command "run" erratic Francesco Pietra (Sun Mar 16 2014 - 14:40:09 CDT)
- Fwd: TCL command "run" erratic Francesco Pietra (Sun Mar 16 2014 - 14:48:12 CDT)
  - Fwd: TCL command "run" erratic Francesco Pietra (Sun Mar 16 2014 - 14:57:53 CDT)
    - Re: Fwd: TCL command "run" erratic Aron Broom (Sun Mar 16 2014 - 15:58:34 CDT)
    - Re: Fwd: TCL command "run" erratic Francesco Pietra (Mon Mar 17 2014 - 02:22:26 CDT)
running benchmarks on NAMD-Lite Hassan Kianinejad (Fri Mar 14 2014 - 17:35:21 CDT)
Generalized Born Implicit solvation with implicit membrane Fotis Baltoumas (Fri Mar 14 2014 - 08:28:45 CDT)
- Re: Generalized Born Implicit solvation with implicit membrane Thomas Evangelidis (Fri Mar 14 2014 - 14:22:36 CDT)
Cross-correlation analysis in multidomain proteins James Starlight (Thu Mar 13 2014 - 05:32:22 CDT)
REï¼š REï¼š Re: REï¼š NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Wed Mar 12 2014 - 09:42:34 CDT)
COLVAR related quesion Abir Ganguly (Tue Mar 11 2014 - 16:06:20 CDT)
- Re: COLVAR related quesion Giacomo Fiorin (Tue Mar 11 2014 - 16:19:24 CDT)
how to get cell vectors in tcl forces script Thomas Evangelidis (Tue Mar 11 2014 - 15:14:17 CDT)
- AW: how to get cell vectors in tcl forces script Norman Geist (Wed Mar 12 2014 - 02:29:43 CDT)
  - RE: how to get cell vectors in tcl forces script Cosseddu, Salvatore (Wed Mar 12 2014 - 07:05:43 CDT)
NAMD on Rescale Istvan Jonyer (Mon Mar 10 2014 - 20:22:10 CDT)
aa_ref-monomer-noh.dcd file in the tutorial of shape-based coarse grained (SBCG) simulation sunyeping (Mon Mar 10 2014 - 20:01:13 CDT)
Call for participation: ISQBP Meeting, Telluride 15-19.06.2014 Vlad Cojocaru (Mon Mar 10 2014 - 11:38:09 CDT)
aa_ref-monomer-noh.dcd in shape-based coarse grained simulation sunyeping (Sat Mar 08 2014 - 20:09:26 CST)
Accelerated Molecular Dynamics logs Johny Telecaster (Sat Mar 08 2014 - 09:37:05 CST)
Regarding colvar distancez Subbarao Kanchi (Sat Mar 08 2014 - 05:00:28 CST)
- RE: Regarding colvar distancez Cosseddu, Salvatore (Sat Mar 08 2014 - 07:44:39 CST)
NAMD 2.9 quits early without error message. Ivan Gregoretti (Fri Mar 07 2014 - 11:36:17 CST)
- Re: NAMD 2.9 quits early without error message. Ivan Gregoretti (Fri Mar 07 2014 - 11:46:54 CST)
- RE: NAMD 2.9 quits early without error message. Morgan, Brittany (Fri Mar 07 2014 - 11:45:15 CST)
  - Re: NAMD 2.9 quits early without error message. Aron Broom (Fri Mar 07 2014 - 17:31:37 CST)
  - Re: NAMD 2.9 quits early without error message. Roy Fernando (Sat Mar 08 2014 - 10:03:21 CST)
    - Re: NAMD 2.9 quits early without error message. Ivan Gregoretti (Mon Mar 10 2014 - 18:45:17 CDT)
Monitoring progress of an ongoing molecular dynamics simulation Ivan Gregoretti (Fri Mar 07 2014 - 08:08:11 CST)
- RE: Monitoring progress of an ongoing molecular dynamics simulation Cosseddu, Salvatore (Fri Mar 07 2014 - 08:21:35 CST)
  - Re: Monitoring progress of an ongoing molecular dynamics simulation Ivan Gregoretti (Fri Mar 07 2014 - 08:52:43 CST)
- RE: Monitoring progress of an ongoing molecular dynamics simulation Bennion, Brian (Fri Mar 07 2014 - 11:44:01 CST)
force field parameter for graphene oxide Asis Jana (Fri Mar 07 2014 - 07:58:34 CST)
- Re: force field parameter for graphene oxide Kenno Vanommeslaeghe (Fri Mar 07 2014 - 11:28:50 CST)
AW: AW: benchmark info Norman Geist (Fri Mar 07 2014 - 01:40:25 CST)
compiling namd-lite Hassan Kianinejad (Thu Mar 06 2014 - 19:08:28 CST)
compiling namd-lite Hassan Kianinejad (Thu Mar 06 2014 - 18:55:54 CST)
How to maintain Density constant? Roy Fernando (Wed Mar 05 2014 - 15:43:59 CST)
- Re: How to maintain Density constant? Kenno Vanommeslaeghe (Wed Mar 05 2014 - 16:51:30 CST)
  - Re: How to maintain Density constant? Ivan Gregoretti (Thu Mar 06 2014 - 07:23:29 CST)
Restarting an FEP simulation Shyno Mathew (Wed Mar 05 2014 - 12:43:48 CST)
- Re: Restarting an FEP simulation Shyno Mathew (Mon Mar 10 2014 - 11:58:02 CDT)
  - Re: Restarting an FEP simulation Shyno Mathew (Sat Mar 22 2014 - 14:00:06 CDT)
VDW energy: positive or negative? PANAGIOTA KYRIAKOU (Tue Mar 04 2014 - 17:20:53 CST)
- Re: VDW energy: positive or negative? Axel Kohlmeyer (Tue Mar 04 2014 - 17:28:08 CST)
- Re: VDW energy: positive or negative? Kenno Vanommeslaeghe (Tue Mar 04 2014 - 17:50:50 CST)
  - Re: VDW energy: positive or negative? PANAGIOTA KYRIAKOU (Tue Mar 04 2014 - 18:24:54 CST)
How to stop omega trans-cis switching Alex Utev (CMP) (Mon Mar 03 2014 - 12:10:08 CST)
- How to stop omega trans-cis switching Alex Utev (CMP) (Mon Mar 03 2014 - 12:11:25 CST)
- Re: How to stop omega trans-cis switching Kenno Vanommeslaeghe (Mon Mar 03 2014 - 13:01:10 CST)
FEP result analysis Javad Noroozi (Sat Mar 01 2014 - 03:37:29 CST)
Generating .psf for amorphous disaccharide Maxwell Wesley Terban (Fri Feb 28 2014 - 13:10:56 CST)
- Re: Generating .psf for amorphous disaccharide JC Gumbart (Sat Mar 01 2014 - 21:41:45 CST)
Apply magnetic field through TCLBC Hongbo Du (Fri Feb 28 2014 - 11:22:04 CST)
- Re: Apply magnetic field through TCLBC Kenno Vanommeslaeghe (Mon Mar 03 2014 - 11:33:06 CST)
  - Re: Apply magnetic field through TCLBC Axel Kohlmeyer (Mon Mar 03 2014 - 11:46:25 CST)
  - RE: Apply magnetic field through TCLBC Hongbo Du (Mon Mar 03 2014 - 16:23:55 CST)
benchmark info Hassan Kianinejad (Thu Feb 27 2014 - 16:34:08 CST)
- AW: benchmark info Norman Geist (Fri Feb 28 2014 - 01:18:46 CST)
solvate plugin watsize value Sridhar Kumar Kannam (Wed Feb 26 2014 - 20:40:46 CST)
Persistent margin errors Vlastimil ZÃma (Wed Feb 26 2014 - 06:38:23 CST)
- Re: Persistent margin errors Vlastimil ZÃma (Wed Apr 16 2014 - 05:28:56 CDT)
  - AW: Re: Persistent margin errors Norman Geist (Wed Apr 16 2014 - 07:49:47 CDT)
Symmetry restraints break IMD handshaking Tristan Croll (Tue Feb 25 2014 - 21:23:26 CST)
ABF simulation fails with "FATAL ERROR: Low global exclusion count!" Maria Pikoula (Tue Feb 25 2014 - 11:02:24 CST)
- Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" Giacomo Fiorin (Tue Feb 25 2014 - 20:19:28 CST)
  - Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" Maria Pikoula (Fri Feb 28 2014 - 11:42:47 CST)
    - Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" JÃ©rÃ´me HÃ©nin (Fri Feb 28 2014 - 11:58:59 CST)
    - Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" Maria Pikoula (Fri Feb 28 2014 - 12:50:27 CST)
Free Energy Perturbation Javad Noroozi (Tue Feb 25 2014 - 00:36:30 CST)
- Re: Free Energy Perturbation JÃ©rÃ´me HÃ©nin (Thu Feb 27 2014 - 07:05:00 CST)
problem compiling NAMD Hassan Kianinejad (Mon Feb 24 2014 - 10:48:51 CST)
- Re: problem compiling NAMD David Hardy (Mon Feb 24 2014 - 13:18:32 CST)
  - Re: problem compiling NAMD David Hardy (Tue Feb 25 2014 - 12:39:11 CST)
    - Re: problem compiling NAMD Ivan Gregoretti (Tue Feb 25 2014 - 13:23:23 CST)
ç”å¤ï¼šREï¼š NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Mon Feb 24 2014 - 03:37:02 CST)
- Re: ´ð¸´£ºRE£º NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance Axel Kohlmeyer (Mon Feb 24 2014 - 04:34:22 CST)
REï¼š Re: REï¼š NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Mon Feb 24 2014 - 03:32:06 CST)
REï¼š NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Sun Feb 23 2014 - 21:13:52 CST)
- Re: RE£º NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance Axel Kohlmeyer (Sun Feb 23 2014 - 21:26:40 CST)
NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Sun Feb 23 2014 - 20:29:02 CST)
- Re: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance Axel Kohlmeyer (Sun Feb 23 2014 - 20:57:18 CST)
Error when running MIC version of namd on Stampede Chen Wei (Fri Feb 21 2014 - 09:49:38 CST)
NAMD 2.9 Changing/Replacing atoms in multiple molecules Michal Skoczek (Fri Feb 21 2014 - 08:02:41 CST)
- Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules Axel Kohlmeyer (Fri Feb 21 2014 - 08:11:33 CST)
  - Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules Kenno Vanommeslaeghe (Fri Feb 21 2014 - 12:38:25 CST)
    - Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules Tristan Croll (Fri Feb 21 2014 - 16:04:43 CST)
FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE zeynab mohamad hoseyni (Thu Feb 20 2014 - 13:31:50 CST)
runaway minimizations Bennion, Brian (Thu Feb 20 2014 - 12:06:54 CST)
About keep_water_out.tcl zeynab mohamad hoseyni (Thu Feb 20 2014 - 05:21:23 CST)
tools for Charmm Peter Reinke (Thu Feb 20 2014 - 02:39:59 CST)
- Re: tools for Charmm Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:16:40 CST)
  - Using nodelist file causes namd to hang Douglas Houston (Tue Apr 08 2014 - 04:29:34 CDT)
- Re: tools for Charmm Gianluca Interlandi (Thu Feb 20 2014 - 12:08:24 CST)
  - Re: tools for Charmm Kenno Vanommeslaeghe (Thu Feb 20 2014 - 13:05:13 CST)
Charmm Peter Reinke (Thu Feb 20 2014 - 02:31:35 CST)
- Re: Charmm Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:40:41 CST)
  - Re: Charmm Gianluca Interlandi (Thu Feb 20 2014 - 12:10:22 CST)
    - Re: Charmm Kenno Vanommeslaeghe (Thu Feb 20 2014 - 12:53:55 CST)
(no subject) Boyang Wang (Thu Feb 20 2014 - 00:05:03 CST)
- Re: write pdb bay__gulf618_at_sina.com (Thu Feb 20 2014 - 00:31:36 CST)
- AW: Norman Geist (Thu Feb 20 2014 - 00:41:55 CST)
Require Suggestion amit banerjee (Tue Feb 18 2014 - 23:39:40 CST)
- AW: Require Suggestion Norman Geist (Wed Feb 19 2014 - 01:42:09 CST)
pThr topology ÂÀÐ¡Ó¨ (Tue Feb 18 2014 - 21:05:27 CST)
protein-membrane interface hydration zeynab mohamad hoseyni (Tue Feb 18 2014 - 13:37:30 CST)
GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance Pino, James Christopher (Tue Feb 18 2014 - 12:00:34 CST)
- AW: GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance Norman Geist (Wed Feb 19 2014 - 01:38:53 CST)
Polarization effect of gold cluster Zhao Lina (Tue Feb 18 2014 - 06:20:20 CST)
- Re: Polarization effect of gold cluster Axel Kohlmeyer (Tue Feb 18 2014 - 06:32:07 CST)
  - Re: Polarization effect of gold cluster Zhao Lina (Fri Feb 21 2014 - 06:30:34 CST)
Failure of namd2.10 in keeping trace of cell in t-remd Francesco Pietra (Tue Feb 18 2014 - 05:44:34 CST)
- Fwd: Failure of namd2.10 in keeping trace of cell in t-remd Francesco Pietra (Tue Feb 18 2014 - 12:45:35 CST)
CHARMM36 and NAMD Douglas Houston (Tue Feb 18 2014 - 04:02:38 CST)
- Re: CHARMM36 and NAMD Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:23:37 CST)
REMD Boshra Moradi (Tue Feb 18 2014 - 02:08:53 CST)
- AW: REMD Norman Geist (Tue Feb 18 2014 - 02:59:07 CST)
ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG! Miss. State (Mon Feb 17 2014 - 17:05:09 CST)
- Re: ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG! Axel Kohlmeyer (Mon Feb 17 2014 - 17:26:41 CST)
  - Re: ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG! Axel Kohlmeyer (Mon Feb 17 2014 - 21:39:00 CST)
atomselect option for extracting protein-ligand complex KK R (Mon Feb 17 2014 - 16:16:43 CST)
- Re: atomselect option for extracting protein-ligand complex Axel Kohlmeyer (Mon Feb 17 2014 - 16:22:38 CST)
Membrane and NPAT José Villalaín (Mon Feb 17 2014 - 04:49:08 CST)
- Re: Membrane and NPAT Kenno Vanommeslaeghe (Mon Feb 17 2014 - 10:43:03 CST)
  - RE: Membrane and NPAT hannes.loeffler_at_stfc.ac.uk (Mon Feb 17 2014 - 10:53:49 CST)
Widom test particle insertion in NAMD Javad Noroozi (Mon Feb 17 2014 - 00:40:08 CST)
Guideline for selecting water box size. Hyuntae Na (Sun Feb 16 2014 - 18:49:00 CST)
- Re: Guideline for selecting water box size. Aron Broom (Sun Feb 16 2014 - 19:12:30 CST)
FAD topology and parameters Tanner, John J. (Sun Feb 16 2014 - 15:30:38 CST)
- Re: FAD topology and parameters flavio seixas (Mon Feb 17 2014 - 06:01:14 CST)
  - Re: FAD topology and parameters Tanner, John J. (Mon Feb 17 2014 - 10:15:52 CST)
    - Re: FAD topology and parameters Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:01:28 CST)
Instability in thermodynamic integration Maryam Sayadi (Sun Feb 16 2014 - 14:04:12 CST)
psf file does not contain cross-terms zeynab mohamad hoseyni (Sun Feb 16 2014 - 12:00:30 CST)
- Re: psf file does not contain cross-terms Axel Kohlmeyer (Sun Feb 16 2014 - 12:10:01 CST)
Adding hydrogen atoms to the crystall structure zeynab mohamad hoseyni (Sun Feb 16 2014 - 09:54:40 CST)
- Re: Adding hydrogen atoms to the crystall structure MEHRAN MB (Tue Feb 18 2014 - 10:10:53 CST)
  - Re: Adding hydrogen atoms to the crystall structure Thomas Evangelidis (Tue Feb 18 2014 - 10:44:56 CST)
  - Re: Adding hydrogen atoms to the crystall structure zeynab mohamad hoseyni (Tue Feb 18 2014 - 14:30:00 CST)
Non standar solvent Javad Noroozi (Sat Feb 15 2014 - 06:52:17 CST)
- Re: Non standar solvent MEHRAN MB (Tue Feb 18 2014 - 10:12:26 CST)
  - Re: Non standar solvent Roy Fernando (Tue Feb 18 2014 - 10:49:10 CST)
    - Re: Non standar solvent bdrakuli (Tue Feb 18 2014 - 11:43:58 CST)
Solvation in non standard solvent Javad Noroozi (Fri Feb 14 2014 - 05:58:59 CST)
Re: Job script for multi node job Subbarao Kanchi (Fri Feb 14 2014 - 05:22:55 CST)
- AW: Job script for multi node job Norman Geist (Fri Feb 14 2014 - 06:03:47 CST)
- Re: Job script for multi node job Subbarao Kanchi (Fri Feb 14 2014 - 08:24:13 CST)
Job script for multi node job Subbarao Kanchi (Fri Feb 14 2014 - 04:20:16 CST)
- AW: Job script for multi node job Norman Geist (Fri Feb 14 2014 - 05:12:56 CST)
- Re: Job script for multi node job Phil Greer (Fri Feb 14 2014 - 09:04:37 CST)
ABF force distribution Kasra Fattah (Thu Feb 13 2014 - 14:56:42 CST)
- Re: ABF force distribution MEHRAN MB (Tue Feb 18 2014 - 10:50:59 CST)
  - Re: ABF force distribution JÃ©rÃ´me HÃ©nin (Thu Feb 27 2014 - 06:59:48 CST)
    - Re: ABF force distribution Kasra Fattah (Sat Mar 01 2014 - 18:20:11 CST)
moving out of the box Ariel Talavera Perez (Thu Feb 13 2014 - 09:57:16 CST)
- Re: moving out of the box Ajasja LjubetiÄ (Thu Feb 13 2014 - 10:08:36 CST)
  - Re: moving out of the box Aaron Larsen (Thu Feb 13 2014 - 14:39:04 CST)
- AW: moving out of the box Norman Geist (Thu Feb 13 2014 - 14:21:26 CST)
  - Re: AW: moving out of the box Ariel Talavera Perez (Fri Feb 14 2014 - 08:38:01 CST)
- AW: moving out of the box Norman Geist (Thu Feb 13 2014 - 14:24:53 CST)
Dihedrals multiplicity! Anna Borlsky (Thu Feb 13 2014 - 09:24:46 CST)
- Re: Dihedrals multiplicity! Jeffrey Potoff (Thu Feb 13 2014 - 10:51:12 CST)
  - Re: Dihedrals multiplicity! Jeffrey Potoff (Thu Feb 13 2014 - 11:34:16 CST)
non-planarity problem! NOE restraints! Anna Borlsky (Thu Feb 13 2014 - 09:22:43 CST)
chloromethyl ketone patch? Jesper Madsen (Tue Feb 11 2014 - 16:49:21 CST)
Determining HIS protonation state using PropKa vmd plug-in zeynab mohamad hoseyni (Tue Feb 11 2014 - 06:30:09 CST)
Questions on calling external program to calculate force with NAMD Wasut Pornpatcharapong (Mon Feb 10 2014 - 15:41:48 CST)
Volume Entry Rawan Al Nsour (Mon Feb 10 2014 - 10:08:19 CST)
- Re: Volume Entry Axel Kohlmeyer (Mon Feb 10 2014 - 10:12:49 CST)
  - Re: Volume Entry Axel Kohlmeyer (Mon Feb 10 2014 - 10:45:37 CST)
PREMD in NAMD Matthew Ralph Adendorff (Mon Feb 10 2014 - 09:27:15 CST)
ABF simulations Abir Ganguly (Sat Feb 08 2014 - 15:38:01 CST)
- Re: ABF simulations Aron Broom (Mon Feb 10 2014 - 11:20:54 CST)
  - Re: ABF simulations Abir Ganguly (Thu Feb 13 2014 - 22:50:10 CST)
    - Re: ABF simulations Aron Broom (Fri Feb 14 2014 - 07:34:46 CST)
    - Re: ABF simulations MEHRAN MB (Tue Feb 18 2014 - 10:38:25 CST)
Log file is not being updated BATUHAN KAV (Mon Feb 10 2014 - 05:41:07 CST)
- Re: Log file is not being updated Ajasja LjubetiÄ (Mon Feb 10 2014 - 05:53:39 CST)
Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Sun Feb 09 2014 - 23:49:41 CST)
- RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Mon Feb 10 2014 - 00:20:57 CST)
  - RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Mon Feb 10 2014 - 18:24:37 CST)
Interactive molecular dynamics question Mare Libero (Sun Feb 09 2014 - 15:05:51 CST)
- Re: Interactive molecular dynamics question Chris Harrison (Sun Feb 09 2014 - 17:00:27 CST)
- Re: Interactive molecular dynamics question Axel Kohlmeyer (Sun Feb 09 2014 - 17:13:15 CST)
Specific Heat Calculation Rawan Al Nsour (Fri Feb 07 2014 - 20:56:14 CST)
Calculating density for a molecule Research Jubilant (Fri Feb 07 2014 - 11:36:41 CST)
- Re: Calculating density for a molecule Jeffrey Potoff (Fri Feb 07 2014 - 13:17:17 CST)
RSMDTT keyword for nucleic acids Aaron Larsen (Wed Feb 05 2014 - 14:43:13 CST)
PMEGridSizeX (number of grid points) is very small. Rawan Al Nsour (Wed Feb 05 2014 - 12:00:57 CST)
- RE: PMEGridSizeX (number of grid points) is very small. Bennion, Brian (Wed Feb 05 2014 - 12:28:37 CST)
  - Re: PMEGridSizeX (number of grid points) is very small. Maxim Belkin (Wed Feb 05 2014 - 12:44:35 CST)
    - Re: PMEGridSizeX (number of grid points) is very small. Aron Broom (Wed Feb 05 2014 - 15:10:53 CST)
Umbrella sampling using colvarconfig file with dihedrals Aaron Larsen (Wed Feb 05 2014 - 11:07:23 CST)
- Re: Umbrella sampling using colvarconfig file with dihedrals Giacomo Fiorin (Wed Feb 05 2014 - 11:25:36 CST)
- Re: Umbrella sampling using colvarconfig file with dihedrals Aron Broom (Wed Feb 05 2014 - 11:27:27 CST)
Question regarding loss of translational entropy calculation in FEP tutorial Monika Sharma (Tue Feb 04 2014 - 14:05:49 CST)
- Re: Question regarding loss of translational entropy calculation in FEP tutorial Aron Broom (Tue Feb 04 2014 - 14:22:31 CST)
- Re: Question regarding loss of translational entropy calculation in FEP tutorial Sunhwan Jo (Tue Feb 04 2014 - 14:47:17 CST)
ERROR: CALCULATED VDWA/B FORCES DOES NOT MATCH ENERGY Shalton Evans (Mon Feb 03 2014 - 21:13:41 CST)
Umbrella Sampling of Sugar Pseudorotation Aaron Larsen (Mon Feb 03 2014 - 13:32:45 CST)
- Re: Umbrella Sampling of Sugar Pseudorotation Dan F. X. Martingano (Mon Feb 03 2014 - 13:40:08 CST)
  - Re: Umbrella Sampling of Sugar Pseudorotation Aron Broom (Mon Feb 03 2014 - 15:01:34 CST)
    - Re: Umbrella Sampling of Sugar Pseudorotation Aaron Larsen (Mon Feb 03 2014 - 15:47:38 CST)
Hydration of protein-lipid interface zeynab mohamad hoseyni (Mon Feb 03 2014 - 10:27:20 CST)
problems about new molecule parameterization Tian Li (Thu Jan 30 2014 - 22:28:36 CST)
Structure size limitation in NAMD Nithyanan Annamalai (Wed Jan 29 2014 - 20:36:54 CST)
- Re: Structure size limitation in NAMD Axel Kohlmeyer (Wed Jan 29 2014 - 21:00:46 CST)
  - Re: Structure size limitation in NAMD Chris Harrison (Wed Jan 29 2014 - 23:41:09 CST)
ERROR: Molecule destroyed by fatal error Marlet Martinez (Mon Jan 27 2014 - 13:31:18 CST)
- Re: ERROR: Molecule destroyed by fatal error Axel Kohlmeyer (Mon Jan 27 2014 - 13:37:58 CST)
Steering colvars to defined points in space Tristan Croll (Sun Jan 26 2014 - 18:10:03 CST)
- Re: Steering colvars to defined points in space Aron Broom (Sun Jan 26 2014 - 19:23:56 CST)
  - RE: Steering colvars to defined points in space Tristan Croll (Sun Jan 26 2014 - 22:44:09 CST)
About Number of atoms in fixed atoms PDB doesn't match coordinate PDB Vidhya Sankar (Sat Jan 25 2014 - 21:01:01 CST)
- Re: About Number of atoms in fixed atoms PDB doesn't match coordinate PDB Sridhar Kumar Kannam (Sat Jan 25 2014 - 23:49:47 CST)
How to solvate a protein using C36 and not C27 zeynab mohamad hoseyni (Sat Jan 25 2014 - 11:08:14 CST)
PMF calculation crashes with constraint failure Magnus Andersson (Sat Jan 25 2014 - 11:02:11 CST)
- Re: PMF calculation crashes with constraint failure Giacomo Fiorin (Sun Jan 26 2014 - 15:37:10 CST)
How to solvate a protein using C36 and not C27 zeynab mohamad hoseyni (Sat Jan 25 2014 - 10:48:31 CST)
Liquid Simulation Failure Roy Fernando (Fri Jan 24 2014 - 18:54:44 CST)
AW: recent comparison of NAMD to other MD engines Norman Geist (Fri Jan 24 2014 - 13:22:51 CST)
recent comparison of NAMD to other MD engines Bennion, Brian (Wed Jan 22 2014 - 18:22:03 CST)
- Re: recent comparison of NAMD to other MD engines Giacomo Fiorin (Wed Jan 22 2014 - 20:38:29 CST)
  - AW: recent comparison of NAMD to other MD engines Norman Geist (Thu Jan 23 2014 - 01:32:54 CST)
  - Re: recent comparison of NAMD to other MD engines Hannes Loeffler (Thu Jan 23 2014 - 04:05:18 CST)
    - Re: recent comparison of NAMD to other MD engines JC Gumbart (Thu Jan 23 2014 - 11:14:22 CST)
    - AW: recent comparison of NAMD to other MD engines Norman Geist (Fri Jan 24 2014 - 01:01:04 CST)
- RE: recent comparison of NAMD to other MD engines Tristan Croll (Fri Jan 24 2014 - 02:44:05 CST)
  - RE: recent comparison of NAMD to other MD engines Bennion, Brian (Fri Jan 24 2014 - 12:59:21 CST)
- unsubscribe Zailo Leite (Fri Feb 14 2014 - 11:20:04 CST)
  - Re: unsubscribe MEHRAN MB (Fri Feb 14 2014 - 11:33:01 CST)
subscribe namd-l Ana Celia Vila Verde (Tue Jan 21 2014 - 11:22:15 CST)
Citating colvars module Salvatore Mario Cosseddu (Tue Jan 21 2014 - 11:20:50 CST)
- Re: Citating colvars module Giacomo Fiorin (Tue Jan 21 2014 - 11:12:55 CST)
Various questions Douglas Houston (Tue Jan 21 2014 - 09:42:14 CST)
- AW: Various questions Norman Geist (Wed Jan 22 2014 - 02:42:07 CST)
  - Re: AW: Various questions Douglas Houston (Wed Jan 22 2014 - 04:30:17 CST)
- Re: Various questions Douglas Houston (Wed Jan 22 2014 - 08:31:03 CST)
  - Re: Various questions Douglas Houston (Mon Feb 03 2014 - 03:52:42 CST)
    - AW: Re: Various questions Norman Geist (Mon Feb 03 2014 - 04:34:48 CST)
    - Re: AW: Re: Various questions Douglas Houston (Tue Feb 04 2014 - 07:26:05 CST)
Question regarding reverse CG to all-atom parikshit moitra (Tue Jan 21 2014 - 04:42:04 CST)
- AW: Question regarding reverse CG to all-atom Norman Geist (Tue Jan 21 2014 - 06:18:10 CST)
Reassure fluctuations in course of simulation James Starlight (Mon Jan 20 2014 - 03:19:51 CST)
Tct script for energy estimation James Starlight (Mon Jan 20 2014 - 03:16:23 CST)
Question regarding loss of translational entropy calculation in FEP tutorial Monika Sharma (Sun Jan 19 2014 - 11:32:02 CST)
About Psfgen error for Lipid molecules Vidhya Sankar (Sun Jan 19 2014 - 07:29:51 CST)
How to parametrize new atom types in Namd Dian Jiao (Fri Jan 17 2014 - 15:44:50 CST)
Re: namd-l digest V1 #1282 Istvan Jonyer (Fri Jan 17 2014 - 14:04:39 CST)
AW: keeping Crystal angles constant Norman Geist (Thu Jan 16 2014 - 02:36:51 CST)
keeping Crystal angles constant Mohan maruthi sena (Wed Jan 15 2014 - 12:03:58 CST)
- AW: keeping Crystal angles constant Norman Geist (Thu Jan 16 2014 - 02:13:08 CST)
RDF calculation with NAMD Dian Jiao (Tue Jan 14 2014 - 15:05:32 CST)
- Re: RDF calculation with NAMD Ana Celia Vila Verde (Tue Jan 21 2014 - 11:23:57 CST)
colvars with replica exchange molecular dynamics Francesco Pietra (Mon Jan 13 2014 - 14:29:41 CST)
- Re: colvars with replica exchange molecular dynamics Giacomo Fiorin (Mon Jan 13 2014 - 15:17:25 CST)
  - Re: colvars with replica exchange molecular dynamics Francesco Pietra (Tue Jan 14 2014 - 02:25:19 CST)
useGroupPressure Anna Borlsky (Fri Jan 10 2014 - 17:09:32 CST)
periodic boundary conditions Anna Borlsky (Fri Jan 10 2014 - 15:27:34 CST)
Thermodynamic integration questions Randall Hall (Thu Jan 09 2014 - 12:16:03 CST)
Difficulties with using the "rescalevels" command every MD timestep Spencer, Jacob (Thu Jan 09 2014 - 09:48:37 CST)
whidth value of orientation in colvars ¼¿ëÀÏ (Thu Jan 09 2014 - 02:27:59 CST)
- Re: whidth value of orientation in colvars Giacomo Fiorin (Thu Jan 09 2014 - 07:31:15 CST)
  - Re: whidth value of orientation in colvars ¼¿ëÀÏ (Thu Jan 09 2014 - 18:28:22 CST)
    - Re: whidth value of orientation in colvars Giacomo Fiorin (Fri Jan 10 2014 - 16:20:45 CST)
MD simulation Patch grid errors Jiann George Pazhamalil (Tue Jan 07 2014 - 17:33:06 CST)
- Re: MD simulation Patch grid errors Thomas Evangelidis (Tue Jan 07 2014 - 17:56:32 CST)
- Re: MD simulation Patch grid errors Jeffrey Potoff (Tue Jan 07 2014 - 18:03:29 CST)
  - Re: MD simulation Patch grid errors Jiann George Pazhamalil (Mon Jan 13 2014 - 21:37:41 CST)
    - Re: MD simulation Patch grid errors Jeffrey Potoff (Mon Jan 13 2014 - 22:34:42 CST)
    - Re: MD simulation Patch grid errors Thomas Evangelidis (Tue Jan 14 2014 - 02:19:55 CST)
CAN'T FIND DIHEDRAL PARAMETERS FOR CPH1 NR2 FE NPH Katherine Parra Pulido (Mon Jan 06 2014 - 23:33:49 CST)
- Re: CAN'T FIND DIHEDRAL PARAMETERS FOR CPH1 NR2 FE NPH Roy Fernando (Tue Jan 07 2014 - 08:05:22 CST)
citing SODIUM program Shyno Mathew (Sat Jan 04 2014 - 10:45:36 CST)
- Re: vmd-l: citing SODIUM program John Stone (Tue Jan 14 2014 - 09:19:27 CST)
About Warning in compilation of Namd Vidhya Sankar (Sat Jan 04 2014 - 03:41:57 CST)
- Re: About Warning in compilation of Namd Axel Kohlmeyer (Sat Jan 04 2014 - 06:21:55 CST)
question about force constant Lurong Pan (Fri Jan 03 2014 - 09:02:13 CST)
PBC only along the z axis. Sridhar Kumar Kannam (Thu Jan 02 2014 - 21:46:58 CST)
- Re: PBC only along the z axis. Subbarao Kanchi (Fri Jan 03 2014 - 00:18:53 CST)
  - Re: PBC only along the z axis. David Hardy (Fri Jan 03 2014 - 17:18:47 CST)
    - Re: PBC only along the z axis. Sridhar Kumar Kannam (Sat Jan 04 2014 - 18:25:28 CST)
About Tcl8.3 error in namd2.8 Vidhya Sankar (Wed Jan 01 2014 - 08:20:20 CST)
- Re: About Tcl8.3 error in namd2.8 Phil Miller (Wed Jan 01 2014 - 09:33:57 CST)
Fwd: Majordomo results Faezeh Mottaghitalab (Wed Jan 01 2014 - 05:19:11 CST)
- Re: Fwd: Majordomo results farzad kiani (Wed Jan 01 2014 - 14:57:29 CST)
  - Re: Fwd: Majordomo results Kuldeep Roy (Wed Jan 01 2014 - 16:33:22 CST)
error : segmentation fault Faezeh Mottaghitalab (Wed Jan 01 2014 - 05:18:30 CST)
Temperature reassignment PANAGIOTA KYRIAKOU (Tue Dec 31 2013 - 11:28:12 CST)
- Re: Temperature reassignment Thomas Evangelidis (Wed Jan 01 2014 - 09:27:57 CST)
  - Re: Temperature reassignment PANAGIOTA KYRIAKOU (Wed Jan 01 2014 - 18:17:40 CST)
    - Re: Temperature reassignment Thomas Evangelidis (Thu Jan 02 2014 - 09:53:35 CST)
    - RE: Temperature reassignment Tristan Croll (Sun Jan 12 2014 - 21:32:03 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)
    - Re: Accelerated MD in NAMD James Starlight (Sat Mar 08 2014 - 09:24:47 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)
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  - 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)
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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)
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)
- Re: grcarma : a graphical user interface to carma Lenin DomÃnguez (Sun Jan 05 2014 - 18:20:50 CST)
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)
  - Re: Boyang Wang (Thu Feb 20 2014 - 00:53:46 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)
Re: Replica-exchange metadynamics scripts Robert Elder (Thu Feb 14 2013 - 18:29:53 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)
RE: reassigning temperatures Martin, Erik W (Thu Jan 03 2013 - 08:19:24 CST)
Issues with the "Keep Water Out" tcl script B Hartzoulakis (Thu Jan 03 2013 - 06:15:50 CST)

Last message date: Tue Dec 30 2014 - 07:38:36 CST
Archived on: Wed Dec 31 2014 - 23:23:10 CST

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