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artificially small???<br><br>I think I will have to read some things about Berendsen and PR.<br><br>Thanks<br>Antonia<br><br>> Date: Tue, 24 Mar 2009 11:09:07 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] (no subject) - fluctuations<br>> <br>> Antonia V. wrote:<br>> > Hello,<br>> > <br>> > I am interested mainly in the density.<br>> > When using parinello-rahman and nose-hoover the fluctuations are <br>> > approximately +/- 8. But when I am using Berendsen it falls to +/- 3.<br>> > I wanted to know if there is a way to reduce the fluctuation width of <br>> > the first case.<br>> <br>> The density fluctuations in Berendsen are artificially small, so PR ones <br>> should be more realistic. This is important when computing properties <br>> like compressibility.<br>> <br>> > <br>> > Antonia<br>> > <br>> > > Date: Tue, 24 Mar 2009 09:49:45 +0100<br>> > > From: spoel@xray.bmc.uu.se<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] (no subject) - fluctuations<br>> > ><br>> > > Antonia V. wrote:<br>> > > > Hello,<br>> > > ><br>> > > > So a I can either increase my system size or do some post<br>> > > > precessing-smoothing...<br>> > ><br>> > > If you elaborate on which properties you are interested in it may be<br>> > > possible to come up with more tips.<br>> > > ><br>> > > > Thanks for the ideas<br>> > > > Antonia<br>> > > ><br>> > > > > Date: Tue, 24 Mar 2009 11:39:19 +1100<br>> > > > > From: Dallas.Warren@pharm.monash.edu.au<br>> > > > > Subject: RE: [gmx-users] (no subject) - fluctuations<br>> > > > > To: gmx-users@gromacs.org<br>> > > > ><br>> > > > > > > Is there a way to reduce the fluctuations of the properties<br>> > > > > > calculated<br>> > > > > > > with g_energy?<br>> > > > ><br>> > > > > > Fluctuations scale as 1/sqrt(N) where N is the number of<br>> > > > > > molecules. So<br>> > > > > > the answer is yes.<br>> > > > ><br>> > > > > Depending on what you actually want to do, some smoothing of the data<br>> > > > > may be what you are after. One way of doing this is taking some <br>> > points<br>> > > > > before and after a time, then averaging them all together.<br>> > > > ><br>> > > > > Catch ya,<br>> > > > ><br>> > > > > Dr. Dallas Warren<br>> > > > > Department of Pharmaceutical Biology and Pharmacology<br>> > > > > Pharmacy and Pharmaceutical Sciences, Monash University<br>> > > > > 381 Royal Parade, Parkville VIC 3010<br>> > > > > dallas.warren@pharm.monash.edu.au<br>> > > > > +61 3 9903 9167<br>> > > > > ---------------------------------<br>> > > > > When the only tool you own is a hammer, every problem begins to <br>> > resemble<br>> > > > > a nail.<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>> > > > Get news, entertainment and everything you care about at Live.com. <br>> > Check<br>> > > > it out! <http://www.live.com/getstarted.aspx ><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>> > > David van der Spoel, Ph.D., Professor of Biology<br>> > > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. 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 <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>> > Get news, entertainment and everything you care about at Live.com. Check <br>> > it out! <http://www.live.com/getstarted.aspx ><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 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>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone:        +46184714205. 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 />check out the rest of the Windows Live™.
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