[gmx-users] Re: Movie from PDB files

Nuno R. L. Ferreira nunolf at ci.uc.pt
Thu Nov 4 22:51:06 CET 2004

----- Original Message ----- 
From: "Gaurav Porwal" <gauravp at che.iitb.ac.in>
To: <gmx-users at gromacs.org>
Sent: Thursday, November 04, 2004 3:54 PM
Subject: [gmx-users] Re: Movie from PDB files

> 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.

Hi Gaurav

So, you have a series of  pdbs's (X files) instead of *one* trajectory file?
Simply concatenate the pdbs and you will get a trajectory, surely VMD is
able to read.
I've done this once, but I don't remember if it was necessary to add a
specific field tag inbetween the pdbs concatenated, in order for VMD to read
the trajectory as containing X frames, instead of reading it as X models.


P.s. If I come to reason, I will post the answer here ;).

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.
> >
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