Hi Tanping, I don't know if that is the problem, but it could be.
I think there was (and still may be) a reproducibility issue when using PME in GROMACS version 3.3.1 combined with FFTW3. See for instance the maillist posts (and subsequent threads) http://www.gromacs.org/pipermail/gmx-developers/2006-December/001986.htm l, http://www.gromacs.org/pipermail/gmx-developers/2007-January/001989.html and http://www.gromacs.org/pipermail/gmx-users/2007-May/027397.html. Some time ago I had the same problem with version 3.3.1 as you described (simulation results changing when only changing output parameters). But at that time I figured it was probably due to the abovementioned PME-issue, and didn't give it much attention. However, I'm definitely not the expert here, so I may be sending you in a totally wrong direction. Especially since you're using the much older 3.2.1 version, of which I don't know whether it has the same issue. So I guess my best advice to you at this moment would be to switch to the newest version (3.3.2) first and check whether the problem persists. Greetings, Jeroen >Date: Mon, 8 Oct 2007 06:07:28 -0700 (PDT) >From: Tanping Li <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Different nstxout and nstvout in mdp file > gives totally different trajectory >To: Discussion list for GROMACS users <[email protected]> >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=iso-8859-1 > >Dear Jeroen, > >I am using gromacs-3.2.1, and PME. Is that the problem? > > >Yours >Tanping > > >--- van Bemmelen ><[EMAIL PROTECTED]> wrote: > >> Hi Tanping, >> >> This may seem irrelevant, but are you using PME? And which >version of >> GROMACS is it? >> >> Greetings, >> Jeroen >> >> >> >Date: Sun, 7 Oct 2007 08:46:04 -0700 (PDT) >> >From: Tanping Li <[EMAIL PROTECTED]> >> >Subject: Re: [gmx-users] Different nstxout and >> nstvout in mdp file >> > gives totally different trajectory >> >To: Discussion list for GROMACS users >> <[email protected]> >> >Message-ID: >> <[EMAIL PROTECTED]> >> >Content-Type: text/plain; charset=iso-8859-1 >> > >> >Dear Tsjerk, >> > >> >Thanks for your help. >> > >> >I run the two jobs on a cluster, maybe on different >> nodes; >> > >> >After just a few hundreds ps, the coordinates of >> the system >> >differs a lot. When I calculate the distance >> between two >> >atoms, there is about 1.5A difference; >> > >> >Everything else in mdp file is exactly same. >> > >> > >> >Yours >> >Tanping _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
