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

PAUL NEWMAN 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


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120207/b2cc7b40/attachment.html>

More information about the gromacs.org_gmx-users mailing list