From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Thu Jul 29 2010 - 14:01:05 CDT
Dear NAMD users,
I have minimized a DNA structure and I am doing equilibration by as a set of restrained simulations in NPT ensemble. I am setting the pressure by using the langevinPiston as below:
## Input files
structure a.psf
coordinates a.pdb
########################################################
set temperature 310
set outputname output
firsttimestep 0
# Input
paraTypeCharmm on
parameters par_all27_na.prm
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
margin 3.0
# 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 49.9 0. 0.
cellBasisVector2 0. 58.5 0.
cellBasisVector3 0. 0. 57.4
cellOrigin 9.96 5.22 7.81
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 45
PMEGridSizeY 54
PMEGridSizeZ 54
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
# langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
constraints on
consexp 2
consref b.pdb
conskfile b.pdb
conskcol B
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Equilibration
numsteps 100000
But, the pressure in the output file is very different from what I defined (1bar)and is not constant at all. I get negative values which are just fluctuating randomly. Any help is really appreciated.
Parisa
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