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<FONT face=Arial>Hi,</FONT><BR>
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<FONT face=Arial>According to Berk's instructions, I first run a 5 ns-long berendesen P-coupling simulation, and then change to Parrinello-Rahman coupling for another 5 ns. The parameters and results are listed in the following. My question is why the average pressures in the X- and Y-directions is not equal to the expected pressure.</FONT><BR>
<FONT face=Arial></FONT> <BR>
<FONT face=Arial>Parameters<BR>================<BR>; Pressure coupling <BR>Pcoupl = Parrinello-Rahman #first using Berendesen<BR>Pcoupltype = semiisotropic<BR>; Time constant (ps), compressibility (1/bar) and reference P (bar)<BR>tau_p = 10<BR>compressibility = 0.0 4.5e-3<BR>ref_p = 300.0 300.0</FONT><BR>
<FONT face=Arial></FONT> <BR>
<FONT face=Arial>Berendesen results<BR>==========================<BR>Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 8 data sets<BR>All averages are exact over 5000001 steps</FONT><BR>
<FONT face=Arial>Energy Average RMSD Fluct. Drift Tot-Drift<BR>-------------------------------------------------------------------------------<BR>Temperature 249.707 2.41024 2.41016 -1.40194e-05 -0.0700972<BR>Pressure (bar) 243.116 121.066 121.063 0.000622752 3.11376<BR>Box-X 2.94006 0 0 0 0<BR>Box-Y 2.94006 0 0 0 0<BR>Box-Z 12.4074 0.125577 0.125523 2.555e-06 0.012775<BR>Pres-XX (bar) 215 201.347 201.317 0.00239071 11.9535<BR>Pres-YY (bar) 214.344 201.326 201.324 -0.000590748 -2.95374<BR>Pres-ZZ (bar) 300.005 178.98 178.98 6.82949e-05 0.341475</FONT><BR>
<FONT face=Arial></FONT> <BR>
<FONT face=Arial>Parrinello-Rahman results<BR>===========================<BR>Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 8 data sets<BR>All averages are exact over 5000001 steps</FONT><BR>
<FONT face=Arial>Energy Average RMSD Fluct. Drift Tot-Drift<BR>-------------------------------------------------------------------------------<BR>Temperature 250.013 2.46785 2.46772 1.72267e-05 0.0861337<BR>Pressure (bar) 241.879 157.901 157.9 -0.000482977 -2.41489<BR>Box-X 2.94006 0 0 0 0<BR>Box-Y 2.94006 0 0 0 0<BR>Box-Z 12.3371 0.146996 0.146474 8.57548e-06 0.0428774<BR>Pres-XX (bar) 210.352 218.481 218.478 -0.000784825 -3.92413<BR>Pres-YY (bar) 215.589 218.513 218.513 -0.000188142 -0.940709<BR>Pres-ZZ (bar) 299.697 236.273 236.272 -0.000475965 -2.37982</FONT><BR>
<BR>
Regards,<BR>
Guang-Jun<BR> <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: Mon, 2 Mar 2009 10:40:47 +0100<BR><BR>
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Hi,<BR><BR>So there is not incorrect coupled pressure at all!<BR>All the coupled directions give the correct pressure.<BR><BR>The Berendsen works and PR not is probably because you have surface as well as a gas.<BR>This makes the system very unstable and PR is not a very stable algorithm.<BR>You first need to equilibrate with Berendsen and then you can switch to PR,<BR>if you use the correct compressibility and a tau_p of around 10.<BR><BR>And, as I said before, with a surface you need to fix the x and y dimensions<BR>(or use surface tension coupling).<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: Mon, 2 Mar 2009 08:14:02 +0000<BR><BR>
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Hi, Berk,<BR> <BR>I once considered what you mention and think it is enough to fix one boxlength (x/y or z) because the volume doesn't diverge. With the P-R and semiisotropy, when fixing z, the Pxx, Pyy, and Pzz are 300.7, 299.8, 393.2. When fixing x/y, the three components are 209.5 224.6, 300.2. You can see the pressures are always right for the coupled direction and are wrong for the fixed one. When all directions are coupled, the three components are 302.7, 297.4, and 300.3 as expected but the box-z increases and box-x/y decreases until the run crashes. Given the phenomenon is caused by the surface tension, why does it not occur with the Berendsen barostat?<BR> <BR>Guang-Jun <BR> <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: 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>
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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: 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>
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