From: Ilya Chorny (ichorny_at_gmail.com)
Date: Fri Oct 05 2007 - 15:02:51 CDT
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.
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