[gmx-users] Gromacs analysis tools for Namd output

PAUL NEWMAN paulclizana at gmail.com
Wed Feb 1 18:35:06 CET 2012

Dear Gromacs 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?

Any help and advise will be highly appreciate it


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