From: Hasan haska (hasanhaska_at_yahoo.com)
Date: Mon Dec 26 2011 - 13:57:37 CST
Dear Namd users,
I run a 5 ns md simulation in NPT ensamble for 1114 glycol molecules to equilibrate the molecules. After the md simulation I looked over the pressure with namdplot and saw that pressure fluctuates between 310743.7 and -1800.41 atm and the averaged fluctuated pressure value is 720 atm which is too high although the target pressure is 1 atm. What is the reason for this ? I attached the out file to the link . Could you please examine these files and control if there is something wrong with my md simulation ?
http://www.mediafire.com/?j08j46vump45j6y
Thanks for your attention.
Best regards.
#--- This is a test namd configuration file
paratypeCharmm on
parameters gyloPRM.prm
structure ETG.psf
coordinates ETG_.pdb
outputName ETGaa1_1out
set temperature 300
temperature $temperature
firsttimestep 0
# Integrator Parameters
timestep 1
nonbondedFreq 1
fullElectFrequency 5
stepspercycle 10
# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.8333333
cutoff 19.7
switching on
switchdist 17
pairlistdist 24
# Constant Temperature Control nvt
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen on ;# don't couple langevin bath to hydrogens
#--- PBC
cellBasisVector1 40. 0.0 0.0
cellBasisVector2 0.0 40. 0.0
cellBasisVector3 0.0 0.0 65.
#--- PME
dielectric 1
PME on
PMEGridSizeX 45
PMEGridSizeY 45
PMEGridSizeZ 72
# Constant presssure Control (variable volume)
useGrouppresssure no ;# needed for 2fs steps
useFlexibleCell yes
useConstantArea yes ;#
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature
#--- Output & ETGtart
binaryoutput no
binaryrestart yes
restartname ETG_1outrestart
DCDfile ETG_1out.dcd
ETGtartfreq 1250
dcdfreq 1250
xstFreq 1250
outputEnergies 1250
forceDCDfreq 1250
outputpresssure 1250
outputtiming 1250
minimize 12500
reinitvels $temperature
run 5000000
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