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<FONT size=3>Hi, </FONT><BR><FONT size=3></FONT> <BR>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT face=Verdana color=#000000 size=3>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). </FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT color=#000000><FONT size=3><FONT face=Verdana> </FONT></FONT></FONT></SPAN></P><SPAN lang=EN-US style="FONT-SIZE: 10.5pt; FONT-FAMILY: 'Times New Roman'"><FONT face=Verdana color=#000000 size=3>Thank you for your kind replies and useful clues.</FONT></SPAN><BR><FONT size=3></FONT> <BR><FONT size=3>Guang-Jun</FONT><BR><FONT size=3></FONT> <BR>
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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: Sat, 28 Feb 2009 15:00:50 +0100<BR><BR>
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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>
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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>
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