[gmx-users] Re: Movie from PDB files

[Robert d'Rozario]

Hi,

One way is to do the following:  Concatenate all your pdb files.  Then
load up vmd: File, new molecule, load, now play your trajectory.  How
many files you have conactenated will be in the counter.  i.e 100 pdbs
will show 100 in the counter place, by the slide bar.  Hope this helps

On Thu, 4 Nov 2004, Gaurav Porwal wrote:

> Dear Kay,
>
> I checked out the VMD site. As far as I can comprehend, VMD can visualize
> the simulation progress if one has a trajectory file generated from any of
> the molecular simulation softwares like gromacs.
>
> What I wanted specifically is that what can be done if one doesn't have
> any trajectory file, instead a few thousand PDB files. One idea is to
> convert all the files to jpeg images and make a movie out of it. If anyone
> can let me know a software that can generate jpeg for such large no. of
> files automatically, then I would be grateful.
>
> Is there any other solution.
>
> Thanks.
> regards,
> Gaurav
>
>
> > Message: 2
> > Date: Wed, 3 Nov 2004 10:56:21 +0200
> > From: Kay Gottschalk <kay.gottschalk at weizmann.ac.il>
> > Subject: Re: [gmx-users] Movie from PDB files
> >
> > VMD does it.
> > K.
> >
>
> _______________________________________________
> 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, 04 Nov 2004 18:15:24
>           +0000
> Received: from tx3.mail.ox.ac.uk by fennel.biop.ox.ac.uk (MX V4.2 AXP) with
>           SMTP; Thu, 04 Nov 2004 18:15:23 +0000
> Received: from scan3.mail.ox.ac.uk ([163.1.2.166] helo=localhost) by
>           tx3.mail.ox.ac.uk with esmtp (Exim 4.42) id 1CPm6Z-0005de-A4 for
>           rozario at biop.ox.ac.uk; Thu, 04 Nov 2004 18:13:03 +0000
> Received: from rx3.mail.ox.ac.uk ([163.1.2.165]) by localhost
>           (scan3.mail.ox.ac.uk [163.1.2.166]) (amavisd-new, port 25) with ESMTP
>           id 21325-04 for <rozario at biop.ox.ac.uk>; Thu,  4 Nov 2004 18:13:02
>           +0000 (GMT)
> Received: from limicola.its.uu.se ([130.238.7.33]) by rx3.mail.ox.ac.uk with
>           esmtp (Exim 4.42) id 1CPm6X-0005cm-AW; Thu, 04 Nov 2004 18:13:01 +0000
> Received: by limicola.its.uu.se (Postfix, from userid 205) id E2D3E488E; Thu, 4
>           Nov 2004 19:13:00 +0100 (MEZ)
> Received: from limicola.its.uu.se(127.0.0.1) by limicola.its.uu.se via
>           virus-scan id s2649; Thu, 4 Nov 04 19:12:52 +0100
> Received: from xray.bmc.uu.se (xray.bmc.uu.se [130.238.41.195]) by
>           limicola.its.uu.se (Postfix) with ESMTP id A5205483F; Thu,  4 Nov
>           2004 19:12:48 +0100 (MEZ)
> Received: from xray.bmc.uu.se (localhost.localdomain [127.0.0.1]) by
>           xray.bmc.uu.se (Postfix) with ESMTP id 012A12519B; Thu,  4 Nov 2004
>           19:12:34 +0100 (CET)
> Received: from limicola.its.uu.se (limicola.its.UU.SE [130.238.7.33]) by
>           xray.bmc.uu.se (Postfix) with ESMTP id CF1812519A for
>           <gmx-users at gromacs.org>; Thu,  4 Nov 2004 19:12:20 +0100 (CET)
> Received: by limicola.its.uu.se (Postfix, from userid 205) id B5C784911; Thu, 4
>           Nov 2004 19:12:20 +0100 (MEZ)
> Received: from limicola.its.uu.se(127.0.0.1) by limicola.its.uu.se via
>           virus-scan id s2808; Thu, 4 Nov 04 19:12:09 +0100
> Received: from smtp2.iitb.ac.in (smtp3.iitb.ac.in [203.199.81.149]) by
>           limicola.its.uu.se (Postfix) with SMTP id 2113F485E for
>           <gmx-users at gromacs.org>; Thu,  4 Nov 2004 19:12:07 +0100 (MEZ)
> Received: (qmail 1498 invoked by uid 780); 4 Nov 2004 15:59:49 -0000
> Received: from 10.102.1.1 by ldns2 (envelope-from <gauravp at che.iitb.ac.in>, uid
>           502) with qmail-scanner-1.23 (spamassassin: 2.64.
>           Clear:RC:1(10.102.1.1):. Processed in 0.017709 secs); 04 Nov 2004
>           15:59:49 -0000
> Received: from unknown (HELO mercury.che.iitb.ac.in) (10.102.1.1) by
>           smtp2.iitb.ac.in with SMTP; 4 Nov 2004 15:59:49 -0000
> Received: from venus.che.iitb.ac.in (venus.che.iitb.ac.in [10.102.1.2]) by
>           mercury.che.iitb.ac.in (MilliardMail daemon) with ESMTP id
>           16AC122E7F8 for <gmx-users at gromacs.org>; Thu,  4 Nov 2004 21:29:49
>           +0530 (IST)
>