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

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Sun Mar 27 2011 - 10:04:35 CDT

Hi Tom,

Could you try a few quick experiments for me?

1) Increase stepsPerCycle to 12 and fullelectfrequency to 3?

2) Lower fullelectfrequency to 1?

3) Turn off PME?

4) Lower langevinDamping to 1?

-Jim

On Thu, 24 Mar 2011, Tom Sisan wrote:

> 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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