VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Apr 29 2007 - 13:41:54 CDT

On Fri, 27 Apr 2007, Marcelo Puiatti wrote:

MP> Dear Users:

dear marcelo,

please avoid cross-postings to mailing lists unless the problem
really affects both communities. usually not all people are not
subscribed to all of the lists and thus a simple reply will always
produce e-mail bounces or requires (annoying) editing of the list
of recipients.

MP> I'm a user of NAMD 2.6 and VMD 1.85.
MP> I'm trying to minimize a protein in a periodic box of 80 x 80 x 150 A,
MP> starting from Amber topologgies and coordinates, but in 2 of my attempts
MP> I've found some weird things.

it is difficult to verify all of your claims from the images,
but to me it seems that you essentially have your protein and
your water box predominantly in difference copies of the principle
unit cell and you don't wrap the coordinates back (sometimes this
is desirable).

the slits in the middle is probably due to the solvate plugin
leaving some safety margin when computing the total box size.

MP> Firts of all, I've constrained the protein and moved only the solvent
MP> molcules, but the solvent box was divided in exatctly 8 parts and nothing
MP> happened to the protein. Each "scrambled" fragment separated by an empty
MP> region passing through the geometric center of the system. However and even
MP> though there were atoms from the solvent too close to the protein, no close
MP> contact messages appeared!!!, more surprisingly the energies were within the
MP> normal values!!!

since every atom will be folded back into the principal unitcell.
you can check this out easily yourself by using the pbctools plugin
(i recommend upgrading to version 1.8.6, as the plugin has been
significantly updated and improved).

MP> See Opt-solv.png
MP>
MP> In the second attempt, the result was slightly different, the water box was
MP> OK, but now the protein was scrambled divided in 8 parts. The solvent box
MP> had a hole where the protein should be placed. Again there were no problems
MP> with the energies, the values obtained were the same as those obtained in a
MP> similar simulation with Amber 7.
MP>
MP> See Min-2.png

this is essentially the same, only with the system shifted by half
a unitcell in each x-,y-, and z-direction.

MP> The atoms move from one corner of the box to the other corner, with a
MP> rotation, or a reflexion. (see file cambio delugar.pdf)
MP> >From the blue corner to the red cornes

if you compare the apparent box size with the real box
that you are using, you'll see that those parts that were
moved are actually outside the normal box.

i suggest you re-evaluate your findings. it seems to me
that the major problem is that your water box and your
protein coordinates have different position w.r.t. the
origin of the box, i.e. one of them is centered around
the origin, the other around the center.

cheers,
  axel.

MP>
MP> See cambio de lugar.pdf
MP>
MP> We've read the coordinates with vmd using both .pdb files, .coord files
MP> (from namd) and we've also attempted to convert .dcd files to Amber with
MP> ptraj, but we allways obtained the same results
MP> As initial input we've used amber files *.top and *.crd as (amber) parmfile
MP> and ambercoor respectively.
MP>
MP>
MP> I presume that there are reading problems between Amber format and namd or
MP> VMD, specially with PBC, however it is quite strange that the energies do
MP> not seem to correspond to the displayed (weird) system.
MP> Exactly the same protocol works fine with several smaller proteins inside an
MP> almost cubic box.
MP>
MP> What is the right protocol to follow in order to run NAMD simulations
MP> starting with Amber files?
MP> Why the same protocol works well with one system and not with another?
MP>
MP>
MP> Marcelo
MP>
MP> P.D.
MP> I attached the .conf file
MP>
MP>
MP> set temperature 300
MP> set outputname Min-2
MP>
MP> firsttimestep 0
MP>
MP> ################################
MP> ## SIMULATION PARAMETERS ##
MP> ################################
MP>
MP> # Input
MP> paraTypeCharmm off
MP> paratypeXplor off
MP> amber on
MP> parmfile Protein.top
MP> ambercoor Protein.crd
MP> temperature $temperature
MP>
MP>
MP> # Force-Field Parameters
MP> exclude scaled1-4
MP> 1-4scaling 0.833333 # =1/1.2, default is 1.0
MP> cutoff 11.5
MP> switching on
MP> switchdist 9.
MP> pairlistdist 13.5
MP>
MP>
MP> # Integrator Parameters
MP> timestep 1.5 ;# 2fs/step
MP> rigidBonds all ;# needed for 2fs steps
MP> nonbondedFreq 1
MP> fullElectFrequency 2
MP> stepspercycle 20
MP>
MP>
MP> # Constant Temperature Control
MP> langevin on ;# do langevin dynamics
MP> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
MP> langevinTemp $temperature
MP> langevinHydrogen off ;# don't couple langevin bath to hydrogens
MP>
MP>
MP> # Periodic Boundary Conditions
MP> cellBasisVector1 80.15 0. 0.
MP> cellBasisVector2 0. 79.24 0.
MP> cellBasisVector3 0. 0.0 150.64
MP> cellOrigin 45.52 45.94 78.17
MP>
MP> wrapAll on
MP>
MP>
MP> # PME (for full-system periodic electrostatics)
MP> PME yes
MP> PMEGridSizeX 144
MP> PMEGridSizeY 144
MP> PMEGridSizeZ 256
MP>
MP>
MP> # Constant Pressure Control (variable volume)
MP> useGroupPressure yes ;# needed for rigidBonds
MP> useFlexibleCell no
MP> useConstantArea no
MP>
MP> # BerendsenPressure on
MP> # BerendsenPressureTarget 1.01325
MP> # BerendsenPressureCompressibility 4.57E-5
MP> # BerendsenPressureRelaxationTime 1000
MP> # BerendsenPressureFreq 20 #chequear
MP>
MP> # langevinPiston on
MP> # langevinPistonTarget 1.01325 ;# in bar -> 1 atm
MP> # langevinPistonPeriod 100.
MP> # langevinPistonDecay 50.
MP> # langevinPistonTemp $temperature
MP>
MP> #Constraints
MP> constraints on
MP> consexp 6
MP> consRef protein.pdb
MP> consKFile protein-constraint.pdb
MP> consKCol B
MP>
MP> # Output
MP> outputName $outputname
MP>
MP> restartfreq 200 ;# 500steps = every 1ps
MP> dcdfreq 500
MP> xstFreq 500
MP> outputEnergies 50
MP> outputPressure 50
MP>
MP> #############################################################
MP> ## EXECUTION SCRIPT ##
MP> #############################################################
MP> # Minimization
MP> minimize 5000
MP> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.