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

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

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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