Re: Charmm 22 vs Charmm 27

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Sat Oct 06 2007 - 11:55:47 CDT

Maybe the problem you are observing is just visualization because you
specify "wrap All". I think this might give the appearance of the protein
breaking apart as part of the protein would be wrapped around the periodic
boundary conditions. If this is the case, I think VMD now has scripts to
unwrap.

If you don't specify "wrap All", the coordinates are stored in the
trajectory as the "actual" coordinates and the protein will appear "whole".
I always store the actual coordinates in case I want to calculate the MSD,
etc. I can always wrap the coordinates in VMD if I want to visualize them
wrapped.

I've never used "wrap All" so maybe I don't understand it well. If I am way
off here, someone please correct me.

Josh

On 10/5/07, Ilya Chorny <ichorny_at_gmail.com> wrote:
>
> Below is configuration file. Does any one see any obvious mistakes? Can
> reinitializing the velocities when I restart a run cause the protein to fall
> apart?
>
> Thanks,
>
> Ilya
>
>
> structure addions.psf
> coordinates addions.pdb
> Bincoordinates Prot_free4.restart.coor
> Binvelocities Prot_free4.restart.vel
> ExtendedSystem Prot_free4.restart.xsc
>
> set temperature 310
> set outputname Prot_free5
> binaryoutput no
>
> #firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters //winsc/share/namd/c31b1/par_all27_prot_lipid.prm
> #temperature $temperature
>
>
> # Force-Field Parameters
> exclude 1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching off
> switchdist 10.5
> pairlistdist 12.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> #cellBasisVector1 117 0. 0.
> #cellBasisVector2 0. 117. 0.
> #cellBasisVector3 0. 0 92.
> #cellOrigin 10.09 9.73 -0.71
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 128
> PMEGridSizeY 128
> PMEGridSizeZ 128
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell yes
> useConstantRatio yes
> zeroMomentum yes
>
> langevinPiston yes
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 100.
> langevinPistonTemp $temperature
>
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 500
> outputPressure 500
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> #Minimization
> #minimize 1000
> # margin 2.5
> reinitvels $temperature
> output NeRh50_free
> #run 2000000 ;# 2ns
> #run 1223500 ;# 2ns
> #run 906500 ;# 2ns
> #run 675500 ;# 2ns
> run 334000 ;# 2ns
>
>
>
>
> On 10/5/07, Ilya Chorny <ichorny_at_gmail.com> wrote:
> >
> > I am running a membrane protein simulation using the CHARMM 27
> > forcefield and I my protein seems to be falling apart. Could it be because I
> > am using CHARMM27 instead of CHARMM22? I am also using TIP3 and POPE.
> >
> > Thanks,
> >
> > Ilya
> >
> >
> > --
> > Ilya Chorny Ph.D.
> >
>
>
>
> --
> Ilya Chorny Ph.D.
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:47:04 CST