Hi, I have been struggling for more than one month with a permanent problem in my simulations. I asked about it in previous mails in this mailing-list. Briefly, the problem is that my simulations crash at some point, and there is nothing explaining it. Nothing but a strange behaviour spotted in msd plot (with g_msd) which show that the motion is somewhat discontinuous, whereas the energies, pressure, temperature are perfectly OK. Recently, I tried this : I ran the files of water simulation of the tutorial (water directory), except I change nsteps = 10000 for nsteps = 1000000 in the grompp.mdp file. That's the only change I made.
And the simulation crashed quickly, for the same reasons. Could anyone try to run this simulation on his computer and tell me whether it works. I really don't understand what is going on. I am using a PowerBookG4, gromacs 3.3.1, my parameters of configuration are : --enable-shared --prefix=%p --exec-prefix=%p --mandir=%p/share --with-external_lapack --with-external_blas Thanks, Michael Bon [EMAIL PROTECTED] -------- Message d'origine-------- De: [EMAIL PROTECTED] de la part de [EMAIL PROTECTED] Date: jeu. 27/09/2007 12:00 À: [email protected] Objet : gmx-users Digest, Vol 41, Issue 88 Send gmx-users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. how to remove periodicity when using g_rmsd (TANG JIAOWEI) 2. Re: how to remove periodicity when using g_rmsd (Florian Haberl) ---------------------------------------------------------------------- Message: 1 Date: Thu, 27 Sep 2007 11:29:59 +0200 From: "TANG JIAOWEI" <[EMAIL PROTECTED]> Subject: [gmx-users] how to remove periodicity when using g_rmsd To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Dear all, I am studying on a big protein with 16 subunits and when i used g_rmsd to one subunit of the protein, the result seems strange that the structure of the subunit changes much but it should not.. I searched the mailing list and it may be caused by the periodic thing. Could you tell me how to remove the periodic thing in detail before i use g_rmsd. Thank you Tang jiaowei -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20070927/00bfec5f/attachment-0001.html ------------------------------ Message: 2 Date: Thu, 27 Sep 2007 11:40:53 +0200 From: Florian Haberl <[EMAIL PROTECTED]> Subject: Re: [gmx-users] how to remove periodicity when using g_rmsd To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="utf-8" Hi, On Thursday, 27. September 2007 11:29, TANG JIAOWEI wrote: > Dear all, > I am studying on a big protein with 16 subunits and when i used g_rmsd to > one subunit of the protein, the result seems strange that the structure of > the subunit changes much but it should not.. I searched the mailing list > and it may be caused by the periodic thing. Could you tell me how to remove > the periodic thing in detail before i use g_rmsd. something like: trjconv -s yourmdstartfile.tpr -f yourtrj.trr -o pbc.trr -pbc nojump select as group your complete system. than g_rmsd ... > > Thank you > > Tang jiaowei Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) â^' 9131 â^' 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- ------------------------------ _______________________________________________ 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! End of gmx-users Digest, Vol 41, Issue 88 *****************************************
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