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Hi,<br><br>Is 327 bar the averge total pressure or one the of components of the pressure tensor?<br>You will have a surface tension acting in the system causing a difference in the different components.<br><br>Also it is still not completely clear to me how long you equilibrate and 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 several ns of equilibration)<br>to obtain a good average.<br><br>Berk<br><br><hr id="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: Sat, 28 Feb 2009 13:51:15 +0000<br><br>
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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 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.<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 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 for water <br>> alone, then the problem likely comes from the inclusion of your gas phase and <br>> whatever parameters you're using for whatever species you have in this phase. <br>> Examine your parameters and consider how they were derived and whether or not <br>> they are adequate.<br>> <br>> Also, what version of Gromacs are you using? There were some changes 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 liquid<br>> > > > water in the NPT ensemble. The temperature is well controlled by using<br>> > > > either the Berendsen or the Nose-Hoover T-couplings. As for 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 produce<br>> > > > the expected pressure with the deviation less than 2 bar. What 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>> > > > 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>> > > >! ! ; 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>> > 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 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/' target='_new'>MSN Messenger</a></body>
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