From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Sun Mar 27 2011 - 10:04:35 CDT
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?
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
> 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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:44 CST