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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 ' target='_new'>立即查看!</a></body>
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