VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Fri Jun 03 2005 - 17:50:51 CDT

The following is an example script I've used to run 50 ps NPT dynamics at 37 C after minimizing the structure for 750 steps. Periodic boundary conditions are used--the basis vectors are the size of your unit cell/box. Parameters in this case are actually spread over two files, which can be nice to separate standard from hacked parameters. "inputname" and "outputname" are variables to set filename stems. Perhaps this will serve as a starting point...

source ./scripts/namdinclude.tcl
set inputname 16_ionized
set outputname ./16_equil_out
set runtype first

margin 5

set checkpointFreq 1000 ;# every 2ps

paraTypeCharmm on
parameters ./common/CHARMM_22prot_27lip.par
parameters ./common/Crclusters.par
coordinates ./$inputname.pdb
structure ./$inputname.psf

# PERIODIC BOUNDARY CONDITIONS

cellBasisVector1 90.35 0. 0.
cellBasisVector2 0. 88.4 0.
cellBasisVector3 0. 0. 94.8
cellOrigin -0.38 -1.80 -8.04 ;# should center coords in PDB...

wrapAll on
wrapWater on

fixedAtoms off

# FORCE-FIELD PARAMS
exclude scaled1-4
1-4scaling 1.0
cutoff 12
switching yes
switchdist 10
pairlistdist 14

# INTEGRATOR PARAMS
rigidBonds all
timestep 2.0
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

#PME ELECTROSTATICS
PME yes
PMEGridSizeX 91
PMEGridSizeY 89
PMEGridSizeZ 96

# TEMPERATURE CONTROL
langevin on ;# do langevin dynamics
langevinDamping 20 ;# initial equilibration
langevinTemp 310.00 ;# bath temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# PRESSURE CONTROL
useGroupPressure yes
useFlexibleCell no
langevinPiston on
langevinPistonTarget 1.01325 # in bar -> 1 atm
langevinPistonPeriod 200 ;# initial equilibration
langevinPistonDecay 100
langevinPistonTemp 310

# OUTPUT
firsttimestep $startingtime
restartname $outputname.restart
outputName $outputname.out
dcdfile $outputname.dcd
xstFile $outputname.xst

xstFreq $checkpointFreq
restartfreq $checkpointFreq
outputEnergies $checkpointFreq
outputPressure $checkpointFreq
dcdfreq $checkpointFreq

# RUN SCRIPT

minimize 750 ;# first time. make it long...
reinitvels 310
set startingtime 0
temperature 310
run 25000 ;# 50ps

Cheers,

Chris

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu]On Behalf
> Of Mark A. Hallman
> Sent: Friday, June 03, 2005 3:01 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: creating scripts
>
>
> Please, forgive my naivete. I wish to run a dynamics
> simulation using NAMD
> with the VMD interface; however, I have no current training
> in computer
> science. I know at which parameters I wish to run my
> simulaitons and what the
> script file should contain, but I do not know how to create
> the actual .conf
> files to set the namd parameters. How do I create script
> files? I have Tcl
> installed on my Win XP system. TIA for any help.
>
> --
> Mark A. Hallman
> 4th-year MSTP
> PhD Candidate
> Cell and Molecular Pharmacology Dept.
> Medical University of South Carolina
>
>