[gmx-users] Re: Gromacs analysis tools for Namd output

Kunze, Micha micha.kunze.10 at ucl.ac.uk
Tue Feb 7 20:04:57 CET 2012

Hey Paul,

cant help you with the plugin issue, but have you instead tried loading the dcd trajectory into vmd and save it as trr?


On 7 Feb 2012, at 18:18, "PAUL NEWMAN" <paulclizana at gmail.com<mailto:paulclizana at gmail.com>> wrote:

Dear Gromacs users,

This is my second email since I tried the previous advises and did NOT work.

I want to use the Gromacs analysis tools for analyzing Namd output files (*.dcd files) I installed Gromacs 4.5.4 (64 bits) and it works well. In addition I installed VMD 1.9 (64 bits) 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

Can anyone tell me if Gromacs really works with the VMD pulgin?

I will highly appreciate to know it so I can start looking for another alternatives.

Thanks so much




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