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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Note that there are proper options for this (no cut-off's):<br>ns_type = simple<br>pbc = none<br></div>nstlist = 0<br>rlist = 0<br>rcoulomb = 0<br>rvdw = 0<br><br>Berk.<br><br><hr id="stopSpelling">> Date: Tue, 20 May 2008 12:45:35 -0700<br>> From: dmobley@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Free energy calculations and speed problems<br>> <br>> Justin and Michael,<br>> <br>> Just to clarify here, I don't think you want the "long cutoff in<br>> vacuum" scheme to give you the same results as the "PME in vacuum"<br>> scheme. That is, if you use PME in vacuum with a periodic box, you<br>> will be including copies of the long-range unscreened electrostatic<br>> interactions between your molecule and its periodic copies. Unless<br>> your box is gigantic, you will probably see significant contributions<br>> to the energy from these. I think for most ordinary vacuum<br>> calculations (i.e. comparing to a vacuum reference state for, say,<br>> hydration free energies) you don't want these contributions and your<br>> desired reference state is something more like the molecule in vacuum,<br>> with no cutoffs, but with no periodic copies. You can achieve that<br>> most easily by simply running in vacuum without pme but making the<br>> cutoffs huge enough to include all of the intramolecular interactions.<br>> Of course, for a protein this would probably be a bad idea for speed<br>> reasons, but for small molecules it can work well.<br>> <br>> David<br>> <br>> <br>> On Tue, May 20, 2008 at 8:06 AM, Justin A. Lemkul <jalemkul@vt.edu> wrote:<br>> ><br>> > Just to follow up - the cutoff scheme worked quite well. It gave me energies<br>> > that were ~1% different from those of the PME calculation, which I think<br>> > compares quite well. The 10-ps run I attempted now takes 3 seconds, instead of<br>> > 20 minutes.<br>> ><br>> > Thanks to everyone for the suggestions.<br>> ><br>> > -Justin<br>> ><br>> > Quoting "Justin A. Lemkul" <jalemkul@vt.edu>:<br>> ><br>> >><br>> >> Thanks to everyone for the insights. I'll try running things with the cutoff<br>> >> and see how it goes.<br>> >><br>> >> -Justin<br>> >><br>> >> Quoting Michael Shirts <mrshirts@gmail.com>:<br>> >><br>> >> > Hi, Justin-<br>> >> ><br>> >> > Have you considered -not- running PME in vacuo? If you set your<br>> >> > cutoffs and rlist large enough, then you can just run with simple<br>> >> > cutoffs, and it should run -faaaast-. Of course, you should compare<br>> >> > to the energy with PME -- if they are not equivalent, then you many<br>> >> > need to go back and check your PME parameters for accuracy.<br>> >> ><br>> >> > Best,<br>> >> > Michael<br>> >> ><br>> >> > > I'm running some free energy calculations (in vacuo and in solution) for<br>> >> a<br>> >> > set<br>> >> > > of molecules I am trying to parameterize. All the molecules are fairly<br>> >> > small,<br>> >> > > about 30-35 atoms in each. The solvated calculations go smoothly, and<br>> >> > rather<br>> >> > > quickly (~5 hr/ns on two nodes). I am running into a problem when I do<br>> >> the<br>> >> > in<br>> >> > > vacuo calculations. Since I am constraining all bonds, I am running<br>> >> things<br>> >> > on<br>> >> > > a local machine in the lab (single core AMD64 Opteron). I get as far as<br>> >> > NVT<br>> >> > > equilibration (removing charges only) before I give up and kill it, since<br>> >> > it<br>> >> > > takes so long. A 10-ps NVT run takes about 20 minutes, but that adds up<br>> >> to<br>> >> > > over 5 days for my 5-ns production run! The machine is no slouch; I have<br>> >> > used<br>> >> > > it to run other small NVT/NPT/MD runs with good performance. I get<br>> >> similar<br>> >> > > performance on another machine that is even faster (a single CPU of the<br>> >> > 2-CPU<br>> >> > > node on our supercomputer). The installations of Gromacs on both are<br>> >> fine,<br>> >> > as<br>> >> > > far as I can tell, and both have been used extensively.<br>> >> > ><br>> >> > > I am using Gromacs version 3.3.3, and I have attached my .mdp file and<br>> >> the<br>> >> > tail<br>> >> > > end of my log file for reference. If anyone notices anything obvious<br>> >> that<br>> >> > I'm<br>> >> > > doing wrong, I would be grateful if you pointed it out! I see in the log<br>> >> > of<br>> >> > > the slow run (in vacuo) that the 3D-FFT calculation is dominating the CPU<br>> >> > > usage. Is that indicative of any problem?<br>> >> > ><br>> >> > > Thanks for your attention.<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>> >><br>> >><br>> >><br>> >> ========================================<br>> >><br>> >> Justin A. Lemkul<br>> >> Graduate Research Assistant<br>> >> Department of Biochemistry<br>> >> Virginia Tech<br>> >> Blacksburg, VA<br>> >> jalemkul@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>> ><br>> ><br>> ><br>> > ========================================<br>> ><br>> > Justin A. Lemkul<br>> > Graduate Research Assistant<br>> > Department of Biochemistry<br>> > Virginia Tech<br>> > Blacksburg, VA<br>> > jalemkul@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>> _______________________________________________<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 />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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