[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system

[Justin A. Lemkul]

GuoGuangjun wrote:
> In fact, I once run the gas-liquid interface for 3 ns, the pressure is 
> still as high as 327 bar.

There are two possibilities in my mind:

1. 3 ns is still not long enough.
2. Your gas phase is causing the problem.  If the pressure is right for water 
alone, then the problem likely comes from the inclusion of your gas phase and 
whatever parameters you're using for whatever species you have in this phase. 
Examine your parameters and consider how they were derived and whether or not 
they are adequate.

Also, what version of Gromacs are you using?  There were some changes made to 
the Parrinello-Rahman barostat between 3.3.x and 4.0.x.

-Justin

> Guang-Jun
> 
>  
>  > Date: Sat, 28 Feb 2009 07:19:30 -0500
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] Cannot obtain the expected pressure using 
> the Parrinello-Rahman coupling in a gas-liquid system
>  >
>  >
>  >
>  > GuoGuangjun wrote:
>  > >
>  > > Hi, All,
>  > > I am simulating an interface system composed of methane gas and liquid
>  > > water in the NPT ensemble. The temperature is well controlled by using
>  > > either the Berendsen or the Nose-Hoover T-couplings. As for pressure,
>  > > the Berendsen P-coupling also works well. However, the 
> Parrinello-Rahman
>  > > P-coupling always produces a higher pressure than the expected. For
>  > > example, I set ref_p=300 bar in the mdp file but obtain an average
>  > > pressure as ~330 bar (over 0.5 ns). I test the tau_p in the range 
> 0.1 ~
>  > > 10 ps, the case does not change. When I test the sin! ! gle-phase 
> system,
>  > > i.e., pure water, the Parrinello-Rahman P-coupling can indeed produce
>  > > the expected pressure with the deviation less than 2 bar. What is the
>  > > matter in the two-phase system?
>  > >
>  >
>  > When I've used the Parrinello-Rahman barostat for membrane systems, 
> it works
>  > just fine. Perhaps 500 ps is too short of a timeframe to arrive at 
> the average.
>  > Heterogeneous systems often take longer to equilibrate.
>  >
>  > -Justin
>  >
>  > > Thanks a lot.
>  > > Guang-Jun
>  > >
>  > > 
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>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Graduate Research Assistant
>  > Department of Biochemistry
>  > Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================