Hi, Justin,
Thanks for your rapid reply. Let me decribes the question in more details.
First ,two gaseous mathane systems and one liquid water system are equilibrated
at 300 bar and 250 K in advance. Then, the gas systems are put at the both
sides of liquid. The combined system is performed for 3ns with the
Parrinello-Rahman barostat, which produces a average pressure of 327 bar. I am
strange to the value and several tests are run, mentioned previously. All these
test runs take the end gro file of the 3ns-run as the beginning. When the
berendsen barostat is used, the pressure is OK. When the Parrinello-Rahman
barostat is used, the questionary pressure occurs again. Although I will try to
make a long run for equilibrium, I think the equilibrium has reached because
the ~330 bar is always obtained no matter how long simulations are sampled,
from 0.2 ns to 3 ns. The version of Gromacs I used is 4.0.4. By the way, how
long did you equilibrate your membrane system and how many atoms in it? Thanks
again.
Guang-Jun
> Date: Sat, 28 Feb 2009 07:43:29 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Cannot obtain the expected pressure using the
> Parrinello-Rahman coupling in a gas-liquid system
>
>
>
> 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: jalem...@vt.edu
> > > To: gmx-users@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
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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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