[gmx-users] (no subject)

[Robert d'Rozario]

Cheers for the responses, I should have told you all that I have computed
the rmsd of my molecule, checked the temperature.  The rmsd completely
levels off very suddenly.  Any other suggestions?

On Thu, 23 Sep 2004, David van der Spoel wrote:

> On Thu, 2004-09-23 at 11:53, Robert d'Rozario wrote:
> > Hi,
> >
> > I was wondering if anyone has this same problem, its a bit worrying.
> > I am simualting an alpha helix in DMSO with PME.  I have 3 separate
> > trajectories, each a continuation.  The first one runs from 0-4ns then
> > 2nd one 4-6ns then the 3rd 6-10ns.  I have then concatenated the files
> > which runs from 0-10ns.  At 6.1 ns I viewed the system, using VMD, and it
> > seems to freeze as if the positon restraints are on everything.
> >
> > Any help would be greatfully appreciated
> start by checking energy terms, temperature,pressure. Then compute a
> mean square displacement for your molecule.
> >
> > Robert D'Rozario
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> --------------------------------------------------------------------------------
> Received: by biop.ox.ac.uk (MX V4.2 AXP) with SITE; Thu, 23 Sep 2004 11:19:22
>           +0100
> Received: from tx1.oucs.ox.ac.uk by fennel.biop.ox.ac.uk (MX V4.2 AXP) with
>           SMTP; Thu, 23 Sep 2004 11:19:20 +0100
> Received: from scan1.oucs.ox.ac.uk ([129.67.1.166] helo=localhost) by
>           tx1.oucs.ox.ac.uk with esmtp (Exim 4.24) id 1CAQh5-0006yy-Hx for
>           rozario at biop.ox.ac.uk; Thu, 23 Sep 2004 11:19:19 +0100
> Received: from rx1.oucs.ox.ac.uk ([129.67.1.165]) by localhost
>           (scan1.oucs.ox.ac.uk [129.67.1.166]) (amavisd-new, port 25) with
>           ESMTP id 26315-06 for <rozario at biop.ox.ac.uk>; Thu, 23 Sep 2004
>           11:19:19 +0100 (BST)
> Received: from limicola.its.uu.se ([130.238.7.33]) by rx1.oucs.ox.ac.uk with
>           esmtp (Exim 4.24) id 1CAQh4-0006yO-5C; Thu, 23 Sep 2004 11:19:18 +0100
> Received: by limicola.its.uu.se (Postfix, from userid 205) id 0A1F7116830; Thu,
>           23 Sep 2004 12:19:17 +0200 (MSZ)
> Received: from limicola.its.uu.se(127.0.0.1) by limicola.its.uu.se via
>           virus-scan id s2816; Thu, 23 Sep 04 12:19:06 +0200
> Received: from xray.bmc.uu.se (xray.bmc.uu.se [130.238.41.195]) by
>           limicola.its.uu.se (Postfix) with ESMTP id 88C3E84012; Thu, 23 Sep
>           2004 12:19:02 +0200 (MSZ)
> Received: from struktbio205.bmc.uu.se (struktbio205.bmc.uu.se [130.238.41.205])
>           by xray.bmc.uu.se (8.11.6/8.8.7) with ESMTP id i8NAAwT17444; Thu, 23
>           Sep 2004 12:10:58 +0200
> Received: from struktbio205.bmc.uu.se (localhost.localdomain [127.0.0.1]) by
>           struktbio205.bmc.uu.se (Postfix) with ESMTP id 2C69824741; Thu, 23
>           Sep 2004 12:12:08 +0200 (CEST)
> Received: from pernis.its.uu.se (pernis.its.UU.SE [130.238.4.153]) by
>           struktbio205.bmc.uu.se (Postfix) with ESMTP id 11AE52473E for
>           <gmx-users at gromacs.org>; Thu, 23 Sep 2004 12:11:55 +0200 (CEST)
> Received: by pernis.its.uu.se (Postfix, from userid 205) id EAD2217596; Thu, 23
>           Sep 2004 12:11:54 +0200 (MSZ)
> Received: from pernis.its.uu.se(127.0.0.1) by pernis.its.uu.se via virus-scan
>           id s394; Thu, 23 Sep 04 12:11:44 +0200
> Received: from xray.bmc.uu.se (xray.bmc.uu.se [130.238.41.195]) by
>           pernis.its.uu.se (Postfix) with ESMTP id CC7CA17591 for
>           <gmx-users at gromacs.org>; Thu, 23 Sep 2004 12:11:44 +0200 (MSZ)
> Received: from [192.168.1.27] (rembrandt.bmc.uu.se [130.238.41.202]) by
>           xray.bmc.uu.se (8.11.6/8.8.7) with ESMTP id i8NAA8T17252 for
>           <gmx-users at gromacs.org>; Thu, 23 Sep 2004 12:10:08 +0200
>