Re: vmd-l: Gromacs analysis tools for Namd output

From: John Stone (
Date: Wed Feb 01 2012 - 11:47:43 CST

  Although we develop all of the VMD plugins here, I don't know much
about the details of how the Gromacs tools have been modified to be able
to use the VMD plugins from the point of view of a user.
If you don't get an answer here on VMD-L in the next day or two,
I would suggest that you ask this question on one of the Gromacs mailing
lists where there may be more people that know the answer.

  John Stone

On Wed, Feb 01, 2012 at 12:41:40PM -0500, PAUL NEWMAN wrote:
> Dear NAMD and VMD users,
> I want to use the Gromacs analysis tools for analyzing Namd output files
> (*.dcd files) I just installed Gromacs 4.5.4 and it works well. In
> addition I installed VMD 1.9 and set up
> VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/ (Here it is
> located the )
> I verified that VMD_PLUGIN_PATH is pointing out to the right folder.
> However when I run for example
> g_rmsf_d -f file.dcd -s file.pdb
> I got the following error
> The file format of file.dcd is not a known trajectory format to GROMACS.
> Please make sure that the file is a trajectory!
> GROMACS will now assume it to be a trajectory and will try to open it
> using the VMD plug-ins.
> This will only work in case the VMD plugins are found and it is a
> trajectory format supported by VMD.
> No plugin for dcd found
> Am I doing something wrong? Do I need to do something else?
> Any help and advise will be highly appreciate it
> Thanks so much for the help
> --
> Cheers,
> Paul

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349       Fax: 217-244-6078

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