VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 02 2004 - 15:50:33 CDT

Dinesh,
  Did you make sure to load a PDB or PSF file with your trajectory?
The various GROMACS trajectory file formats don't include anything but
coordinates if I recall correctly, so you also need to load a PDB in order
to see anything. If you want correct bonding information (rather than
VMD's best guess) then you'll probably want to use this Perl script
to convert the GROMACS topology file to a PSF file that VMD will read:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/

Once you successfully load your structure file and trajectory into VMD,
you will be able to animate it with the animation controls at the bottom
of the main VMD window. If you want to make MPEG movies, you'll want to use
the 'vmdmovie' plugin, and related software packages that you'll need to
install, which are described here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/vmdmovie/

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 02, 2004 at 12:47:58PM -0700, pinisetty dinesh wrote:
> Hi,
> I have two basic questions.
> 1)Is VMD not feasible with .xtc .tpr .trr extensions
> of the GROMACS output files.I tried to read traj.xtc
> which I got as an GROMACS output file but it not read
> it and give me a displayneither it did show me any
> errors.Is there any mistake which I have done or is
> there any way to make VMD read these files.
>
> 2)How to see the whole simulation run as a movie in
> VMD.I want to see the whole 500ps simulation run as a
> movie in VMD,how to make it happen.
> Please bear with me if these questions are petty
> simple.Thanks a lot in advance.........
> Thanking you,
> DINESH.
>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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