[gmx-users] Re: Gromacs analysis tools for Namd output
paulclizana at gmail.com
Tue Feb 7 19:17:44 CET 2012
Dear Gromacs users,
This is my second email since I tried the previous advises and did NOT
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
Thanks so much
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