Re: Gromacs analysis tools for Namd output

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Feb 01 2012 - 11:48:47 CST

On Wed, Feb 1, 2012 at 12:41 PM, PAUL NEWMAN <paulclizana_at_gmail.com> 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  dcdplugin.so )
>
> 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?

paul,

this looks like you should better ask the question
on the gromacs mailing list. does gromacs analysis
tools support molfile plugins? if yes, then the gromacs
folks should be able to tell you how to do this.

axel.

>
> Any help and advise will be highly appreciate it
>
> Thanks so much for the help
>
>
> --
> Cheers,
>
> Paul
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

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