Re: scripiting problem

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Wed Nov 11 2009 - 03:06:05 CST

1/ NAMD input configuration file should not be in MSOffice binary
format. It must be plain text (though there could be other
possiblities in namd that I am unaware)

2/ Your run file could look something like this

#############################################################
## JOB DESCRIPTION ##
#############################################################

# Protein in a Water Box

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure XXX.si.psf
coordinates XXX.si.pdb
#binvelocities XXX.si.vel

set start_temperature 0
set hold_temperature 300
set outputname XXX.md

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ./par_all27_prot_lipid.inp
temperature $start_temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0 #Cutoff-2
pairlistdist 14.0 #Cutoff+2
stepspercycle 10
margin 2.5

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
useSettle on ;#If rigid bonds are enabled use
non-interactive SETTLE alg to keep waters rigid

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinHydrogen no ;# don't couple langevin bath to hydrogens
#langevinTemp $hold_temperature ;#langevin temperature is
defined in protocol section

#Affects the output. Wrapping does not affect the simulation.
wrapWater on
wrapAll on

#Pressure Control
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $hold_temperature

# Periodic Boundary Conditions
cellBasisVector1 80.6570014954 0 0
cellBasisVector2 0 78.6370010376 0
cellBasisVector3 0 0 70.8150005341
cellOrigin 12.0668563843 43.2910957336 16.0740718842

#PME (for full-system periodic electrostatics)
PME yes
#PMEGridSpacing 1.0 ;#Using good default. Let NAMD set the grid.

PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 108

# Output
outputName $outputname

restartfreq 2500
dcdfreq 2500
xstFreq 2500
outputEnergies 2500
outputPressure 2500

#############################################################
## EXTRA PARAMETERS ##
#############################################################

#constraints on

#############################################################

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
#minimize 5000

#RELAXATION PROTOCOL
# 350000 steps
# 140 frames (dcdfreq=2500)
# 700 ps (timestep=2fs)

# Heat +1K in 0.4ps
for { set TEMP $start_temperature } { $TEMP < $hold_temperature } {
incr TEMP 1 } {
        langevinTemp $TEMP
        reinitvels $TEMP
        run 200
}

#Adjust environment to final conditions
langevinTemp $hold_temperature
reinitvels $hold_temperature

#Constraints release protocol

#Free dynamics for 10ns
#constraintScaling 0
run 5000000

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