[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system
David van der Spoel
spoel at xray.bmc.uu.se
Sun Mar 1 11:27:19 CET 2009
GuoGuangjun wrote:
> Hi,
> After I recheck the box, it is indeed the case described in bugzilla
> 165. The length of box increases in the Z-direction and decreases in the
> X/Y-direction with time. When I prolong the run, it exits abnormally at
> the time when the Box-X/Y reduces to a value less than 2*rvdw. When I
> fix the Box-Z by setting the compressibility as zero, the semiisotropic
> with P-R barostat produces the inaccurate pressure again. Now, I have to
> use the Berendsen barostat for my methane-water interface system.
> Guang-Jun
>
OK, good that you checked.
As said we are not sure what is happening with anisotropic or
semi-isotropic pressure scaling. It could be a bug, or a fundamental
error in the algorithm. It would be nice if someone could reproduce this
in another MD program (to see whether it is a bug) or check the
equations of the pressure coupling. Maybe it is due to artificial
breaking up of the Pressure in components.
Note that there also is surface tension coupling (i.e. coupling to (Px +
Py - 2 PZ)/(lZ)). No idea whether that should be better than
semiisotropic, but at least this is a physical quantity.
> > Date: Sat, 28 Feb 2009 19:53:10 +0100
> > From: spoel at xray.bmc.uu.se
> > 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,
> > >
> > >
> > > The question is resolved by changing the pcoupltype from isotropic to
> > > semiisotropic. Correspondingly, the compressibility and ref_p are
> given
> > > for the x/y and z directions with the same original values,
> > > respectively. The test system includes 300 methane, 1725 water, and
> 300
> > > methane, forming two interfaces parallel to the xy-plane. Now, the
> > > accurate average-total-pressure is obtained from a short run (0.2 ns)
> > > with the default tau_p (1 ps).
> >
> > Please be careful when you use this kind of pressure coupling, you may
> > get the right pressure but you box might keep growing in one direction
> > forever. See bugzilla 165. Actually I'm pretty sure it will.
> > Unfortunately we don't really understand what is going on here.
> > >
> > >
> > >
> > > Thank you for your kind replies and useful clues.
> > >
> > > Guang-Jun
> > >
> > >
> ------------------------------------------------------------------------
> > > From: gmx3 at hotmail.com
> > > 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
> > > Date: Sat, 28 Feb 2009 15:00:50 +0100
> > >
> > > Hi,
> > >
> > > Is 327 bar the averge total pressure or one the of components of the
> > > pressure tensor?
> > > You will have a surface tension acting in the system causing a
> > > difference in the different components.
> > >
> > > Also it is still not completely clear to me how long you
> equilibrate and
> > > average.
> > > Also the results will depend very much on the size of the system.
> > > In small systems the pressure fluctuations are enormous.
> > > With Berendsen these fluctuations will be surpressed, with PR not.
> > >
> > > With PR I would use a tau_p of around 10 ps.
> > > You might need to average the pressure over several (tens of?) ns
> (after
> > > several ns of equilibration)
> > > to obtain a good average.
> > >
> > > Berk
> > >
> > >
> ------------------------------------------------------------------------
> > > From: guogj at hotmail.com
> > > 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
> > > Date: Sat, 28 Feb 2009 13:51:15 +0000
> > >
> > > 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: 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.
> > > > > >
> > > > > > -Justin
> > > > > >
> > > > > > > Thanks a lot.
> > > > > > > Guang-Jun
> > > > > > >
> > > > > > >
> > > > >
> > >
> ------------------------------------------------------------------------
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> > > > >
> > >
> ------------------------------------------------------------------------
> > > > > > >
> > > > > > > _______________________________________________
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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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> > >
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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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> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> > _______________________________________________
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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