Re: why pressure is fluctuating so much

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Fri Apr 28 2006 - 00:40:45 CDT

hi,

> I am using a NPT ensemble in PBC condition for my production run.After
> analysis what i observe is that the pressure deviates from -400 to +400
> bar,even though i have given 1 bar in the config file using Langevin
> dynamics.
i think this is quite normal in NPT simulations. pressure changes are
induced by a change in the simulation cell dimensions. due to very low
compressibility of water (i presume you're running simulation in water),
even very small change in volume is accompanied by large change in pressure.
try to do a running average of the pressure curve. i think it will be
fairly close to 1 atm.

> Also the cell volume change by 2/3rd (smaller in volume) after production.
> Prior to this i did equilibriation in NVT ensemble for a fairly long time.
well, after switching from NVT to NPT you can expect some changes in
simulation cell vectors. for example, density of your system in NVT
might have been wrong and it couldn't be changed because both N and T
vere kept constant.
but the change is quite big... maybe you should try to calculate the
density of your system from the nvt and npt simulation vectors and
decide which one is closer to reality...

regards,
lubos

-- 
.....................................................
Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
http://www.molecular.cz/~vrbka
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