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

Berk Hess gmx3 at hotmail.com
Mon Mar 2 08:19:49 CET 2009 

Hi,

Also I don't know what you chose for the compressibility.
In the z direction you mainly compress the gas, not the water.
Therefore the compressibility in z will be orders of magnitude higher
than for water. If you chose the compressibility of water for z,
the fluctuations will be orders of magnitude too slow and you will
probably not equilibrate the box size and pressure in reasonable time.
You can check this by looking at the box dimensions and/or pressure
with g_energy.

Berk

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: Sun, 1 Mar 2009 22:18:51 +0100








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！
> > > > > > <http://im.live.cn/safe/>
> > > > > >
> > > > > >
> > > > > >
> > > > 
> > ------------------------------------------------------------------------
> > > > > >
> > > > > > _______________________________________________
> > > > > >! ! ; gmx-users mailing list gmx-users at gromacs.org
> > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > Please search the archive at http://www.gromacs.org/search before
> > > > posting!
> > > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > > >
> > > > > --
> > > > > ========================================
> > > > >
> > > > > 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
> > > > >
> > > > > ========================================
> > > > > _______________________________________________
> > > > > gmx-users mailing list gmx-users at gromacs.org
> > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > Please! ! search the archive at http://www.gromacs.org/search before
> > > > posting!
> > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > >
> > > > 
> > ------------------------------------------------------------------------
> > > > 你和你的爱人都去过哪里？快来微软地图一起绘制爱的地图吧！ 立即查看！
> > > > <http://ditu.live.com/?form=MICHAJ >
> > >
> > > --
> > > ========================================
> > >
> > > 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
> > >
> > > ========================================
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before 
> > posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > 
> > ------------------------------------------------------------------------
> > 你和你的爱人都去过哪里？快来微软地图一起绘制爱的地图吧！ 立即查看！ 
> > <http://ditu.live.com/?form=MICHAJ>
> > ------------------------------------------------------------------------
> > Express yourself instantly with MSN Messenger! MSN Messenger 
> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> > ------------------------------------------------------------------------
> > MSN 9.0 正式版上线，捆绑免费25G网络硬盘！ 立刻下载！ 
> > <http://im.live.cn/msn9/>
> > 
> > 
> > ------------------------------------------------------------------------
> > 
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> -- 
> 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
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

你和你的爱人都去过哪里？快来微软地图一起绘制爱的地图吧！ 立即查看！
Express yourself instantly with MSN Messenger! MSN Messenger
_________________________________________________________________
See all the ways you can stay connected to friends and family
http://www.microsoft.com/windows/windowslive/default.aspx
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090302/742b4b18/attachment.html>

More information about the gromacs.org_gmx-users mailing list