Why are the pressures in my box of water systematically off?

From: Tom Sisan (tbsisan_at_gmail.com)
Date: Thu Mar 24 2011 - 18:33:39 CDT

Hi all,
I have started simulating boxes of water to try and understand pressure
control. The average output pressures of my simulations (the mean of
GPRESSAVG) are always too high. For a small system, for a target pressure
of 1 atm, the system pressure is consistently about 6 atm. Also, I have
noticed a trend where the smaller my box of water, the bigger the deviation
between the target pressure (langevinPistonTarget) and the average of
GPRESSAVG. Is this behavior expected and understood?

Also, I have not been able to get the output of the pressureProfile to match
with the average of GPRESSAVG. It looked to me like it should just be a
matter of adding the PRESSUREPROFILE output with the ewald PRESSUREPROFILE
output calculated offline as shown in the example in the user guide. But
the ewald contribution is about -200atm for each bin along the z-coordinate,
and the other contributions are about +100atm. I don't understand this
discrepency between the pressure profile and the global pressures
(GPRESSAVG).

Thanks for any help, an example of my config file is below.
-Tom

structure n233watermolecules.psf
coordinates n233watermolecules.pdb

cellBasisVector1 20.0 0.0 0.0
cellBasisVector2 0.0 20.0 0.0
cellBasisVector3 0.0 0.0 20.0
cellOrigin 0.0 0.0 0.0

wrapWater on

exclude scaled1-4
1-4scaling 1.0
cutoff 11.
switching on
switchdist 9.
pairlistdist 14.0

timestep 2.0
rigidBonds water
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

PME yes
PMEGridSizeX 24
PMEGridSizeY 24
PMEGridSizeZ 24

langevin on
langevinDamping 5
langevinTemp 300
langevinHydrogen no

useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp 300

run 2500000

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