[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system
Justin A. Lemkul
jalemkul at vt.edu
Sat Feb 28 15:00:30 CET 2009
GuoGuangjun wrote:
> 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 have 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.
>
What you may want to do is equilibrate the system for a short amount of time
using the Berendsen barostat, then switch to Parrinello-Rahman during data
collection.
This may be a question of magnitude. Your pressure is off by 27 bar, or ~10%.
If you were running under normal conditions (1 bar), and you achieved a pressure
of 1.1 bar, you probably wouldn't be shocked. This may indicate that you need
to run substantially longer to achieve the proper pressure.
My membrane systems are generally upwards of 70,000 atoms, run for 100 ns or
more. The pressure tends to stabilize around the correct value after 10-20 ns.
This may or may not be relevant information in your case.
-Justin
> Guang-Jun
>
> > Date: Sat, 28 Feb 2009 07:43:29 -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:
> > > 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.
> > > &g! ! t;
> > > > -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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--
========================================
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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