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Hi,<br><br>Also I don't know what you chose for the compressibility.<br>In the z direction you mainly compress the gas, not the water.<br>Therefore the compressibility in z will be orders of magnitude higher<br>than for water. If you chose the compressibility of water for z,<br>the fluctuations will be orders of magnitude too slow and you will<br>probably not equilibrate the box size and pressure in reasonable time.<br>You can check this by looking at the box dimensions and/or pressure<br>with g_energy.<br><br>Berk<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system<br>Date: Sun, 1 Mar 2009 22:18:51 +0100<br><br>
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Hi,<br><br>But this has nothing to do with bug 165, does it?<br><br>If you have a surface, you have surface tension which tries to minimize the surface area.<br>That is what you should get and what you indeed do get; x/y get smaller, z gets larger,<br>decreasing the surface area.<br><br>If you have a x/y surface, you should keep the x/y sizes constant and only couple z.<br><br>Berk<br><br><hr id="EC_stopSpelling">From: guogj@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system<br>Date: Sun, 1 Mar 2009 05:09:39 +0000<br><br>
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Hi,<br>
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.<br>
Guang-Jun<br>
<br>> Date: Sat, 28 Feb 2009 19:53:10 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system<br>> <br>> GuoGuangjun wrote:<br>> > Hi,<br>> > <br>> > <br>> > The question is resolved by changing the pcoupltype from isotropic to <br>> > semiisotropic. Correspondingly, the compressibility and ref_p are given <br>> > for the x/y and z directions with the same original values, <br>> > respectively. The test system includes 300 methane, 1725 water, and 300 <br>> > methane, forming two interfaces parallel to the xy-plane. Now, the <br>> > accurate average-total-pressure is obtained from a short run (0.2 ns) <br>> > with the default tau_p (1 ps).<br>> <br>> Please be careful when you use this kind of pressure coupling, you may<br>> get the right pressure but you box might keep growing in one direction<br>> forever. See bugzilla 165. Actually I'm pretty sure it will.<br>> Unfortunately we don't really understand what is going on here.<br>> > <br>> > <br>> > <br>> > Thank you for your kind replies and useful clues.<br>> > <br>> > Guang-Jun<br>> > <br>> > ------------------------------------------------------------------------<br>> > From: gmx3@hotmail.com<br>> > To: gmx-users@gromacs.org<br>> > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the <br>> > Parrinello-Rahman coupling in a gas-liquid system<br>> > Date: Sat, 28 Feb 2009 15:00:50 +0100<br>> > <br>> > Hi,<br>> > <br>> > Is 327 bar the averge total pressure or one the of components of the <br>> > pressure tensor?<br>> > You will have a surface tension acting in the system causing a <br>> > difference in the different components.<br>> > <br>> > Also it is still not completely clear to me how long you equilibrate and <br>> > average.<br>> > Also the results will depend very much on the size of the system.<br>> > In small systems the pressure fluctuations are enormous.<br>> > With Berendsen these fluctuations will be surpressed, with PR not.<br>> > <br>> > With PR I would use a tau_p of around 10 ps.<br>> > You might need to average the pressure over several (tens of?) ns (after <br>> > several ns of equilibration)<br>> > to obtain a good average.<br>> > <br>> > Berk<br>> > <br>> > ------------------------------------------------------------------------<br>> > From: guogj@hotmail.com<br>> > To: gmx-users@gromacs.org<br>> > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the <br>> > Parrinello-Rahman coupling in a gas-liquid system<br>> > Date: Sat, 28 Feb 2009 13:51:15 +0000<br>> > <br>> > Hi, Justin,<br>> > <br>> > Thanks for your rapid reply. Let me decribes the question in more details.<br>> > First ,two gaseous mathane systems and one liquid water system are <br>> > equilibrated at 300 bar and 250 K in advance. Then, the gas systems are <br>> > put at the both sides of liquid. The combined system is performed for <br>> > 3ns with the Parrinello-Rahman barostat, which produces a average <br>> > pressure of 327 bar. I am strange to the value and several tests are <br>> > run, mentioned previously. All these test runs take the end gro file of <br>> > the 3ns-run as the beginning. When the berendsen barostat is used, <br>> > the pressure is OK. When the Parrinello-Rahman barostat is used, the <br>> > questionary pressure occurs again. Although I will try to make a long <br>> > run for equilibrium, I think the equilibrium has reached because the <br>> > ~330 bar is always obtained no matter how long simulations are sampled, <br>> > from 0.2 ns to 3 ns. The version of Gromacs I used is 4.0.4. By the way, <br>> > how long did you equilibrate your membrane system and how many atoms <br>> > in it? Thanks again.<br>> > <br>> > Guang-Jun<br>> > <br>> > <br>> > <br>> > > Date: Sat, 28 Feb 2009 07:43:29 -0500<br>> > > From: jalemkul@vt.edu<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using <br>> > the Parrinello-Rahman coupling in a gas-liquid system<br>> > ><br>> > ><br>> > ><br>> > > GuoGuangjun wrote:<br>> > > > In fact, I once run the gas-liquid interface for 3 ns, the pressure is<br>> > > > still as high as 327 bar.<br>> > ><br>> > > There are two possibilities in my mind:<br>> > ><br>> > > 1. 3 ns is still not long enough.<br>> > > 2. Your gas phase is causing the problem. If the pressure is right <br>> > for water<br>> > > alone, then the problem likely comes from the inclusion of your gas <br>> > phase and<br>> > > whatever parameters you're using for whatever species you have in <br>> > this phase.<br>> > > Examine your parameters and consider how they were derived and <br>> > whether or not<br>> > > they are adequate.<br>> > ><br>> > > Also, what version of Gromacs are you using? There were some changes <br>> > made to<br>> > > the Parrinello-Rahman barostat between 3.3.x and 4.0.x.<br>> > ><br>> > > -Justin<br>> > ><br>> > > > Guang-Jun<br>> > > ><br>> > > ><br>> > > > > Date: Sat, 28 Feb 2009 07:19:30 -0500<br>> > > > > From: jalemkul@vt.edu<br>> > > > > To: gmx-users@gromacs.org<br>> > > > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using<br>> > > > the Parrinello-Rahman coupling in a gas-liquid system<br>> > > > ><br>> > > > ><br>> > > > ><br>> > > > > GuoGuangjun wrote:<br>> > > > > ><br>> > > > > > Hi, All,<br>> > > > > > I am simulating an interface system composed of methane gas and <br>> > liquid<br>> > > > > > water in the NPT ensemble. The temperature is well controlled <br>> > by using<br>> > > > > > either the Berendsen or the Nose-Hoover T-couplings. As for <br>> > pressure,<br>> > > > > > the Berendsen P-coupling also works well. However, the<br>> > > > Parrinello-Rahman<br>> > > > > > P-coupling always produces a higher pressure than the expected. For<br>> > > > > > example, I set ref_p=300 bar in the mdp file but obtain an average<br>> > > > > > pressure as ~330 bar (over 0.5 ns). I test the tau_p in the range<br>> > > > 0.1 ~<br>> > > > > > 10 ps, the case does not change. When I test the sin! ! gle-phase<br>> > > > system,<br>> > > > > > i.e., pure water, the Parrinello-Rahman P-coupling can indeed <br>> > produce<br>> > > > > > the expected pressure with the deviation less than 2 bar. What <br>> > is the<br>> > > > > > matter in the two-phase system?<br>> > > > > ><br>> > > > ><br>> > > > > When I've used the Parrinello-Rahman barostat for membrane systems,<br>> > > > it works<br>> > > > > just fine. Perhaps 500 ps is too short of a timeframe to arrive at<br>> > > > the average.<br>> > > > > Heterogeneous systems often take longer to equilibrate.<br>> > > > ><br>> > > > > -Justin<br>> > > > ><br>> > > > > > Thanks a lot.<br>> > > > > > Guang-Jun<br>> > > > > ><br>> > > > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > > > 立刻下载 MSN 保护盾，保障 MSN 安全稳定！ 现在就下载！<br>> > > > > > <http://im.live.cn/safe/><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > > ><br>> > > > > > _______________________________________________<br>> > > > > >! ! ; gmx-users mailing list gmx-users@gromacs.org<br>> > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > > > > Please search the archive at http://www.gromacs.org/search before<br>> > > > posting!<br>> > > > > > Please don't post (un)subscribe requests to the list. Use the<br>> > > > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > > > ><br>> > > > > --<br>> > > > > ========================================<br>> > > > ><br>> > > > > Justin A. Lemkul<br>> > > > > Graduate Research Assistant<br>> > > > > Department of Biochemistry<br>> > > > > Virginia Tech<br>> > > > > Blacksburg, VA<br>> > > > > jalemkul[at]vt.edu | (540) 231-9080<br>> > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > > > ><br>> > > > > ========================================<br>> > > > > _______________________________________________<br>> > > > > gmx-users mailing list gmx-users@gromacs.org<br>> > > > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > > > Please! ! search the archive at http://www.gromacs.org/search before<br>> > > > posting!<br>> > > > > Please don't post (un)subscribe requests to the list. Use the<br>> > > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > 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！<br>> > > > <http://ditu.live.com/?form=MICHAJ ><br>> > ><br>> > > --<br>> > > ========================================<br>> > ><br>> > > Justin A. Lemkul<br>> > > Graduate Research Assistant<br>> > > Department of Biochemistry<br>> > > Virginia Tech<br>> > > Blacksburg, VA<br>> > > jalemkul[at]vt.edu | (540) 231-9080<br>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > ><br>> > > ========================================<br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the<br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? 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Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br><hr>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！ <a href="http://ditu.live.com/?form=MICHAJ%20">立即查看！</a><br><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/">MSN Messenger</a><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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