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

Berk Hess gmx3 at hotmail.com
Sun Mar 1 22:18:51 CET 2009 

Hi,

But this has nothing to do with bug 165, does it?

If you have a surface, you have surface tension which tries to minimize the surface area.
That is what you should get and what you indeed do get; x/y get smaller, z gets larger,
decreasing the surface area.

If you have a x/y surface, you should keep the x/y sizes constant and only couple z.

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: Sun, 1 Mar 2009 05:09:39 +0000








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

 
> 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
> > > > > >
> > > > > >
> > > > 
> > ------------------------------------------------------------------------
> > > > > > 立刻下载 MSN 保护盾，保障 MSN 安全稳定！ 现在就下载！
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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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