From: Hasan haska (hasanhaska_at_yahoo.com)
Date: Wed Dec 28 2011 - 02:18:30 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 ?
Could
you please make an explanation about this issue ?
Thank
you very much 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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