[gmx-users] How to set the VMD_PLUGIN_PATH for gromacs analysis?

a a patd_2 at hotmail.com
Sat Mar 31 05:47:28 CEST 2012

Dear Sir/Madam,
I am trying to run covar using mdcrd file.
I installed the vmd and gromacs 4.5.5. to my computer. I also set the VMD_PLUGIN_PATH by adding a line in .bashrc file in my home directory.
When I did the following command: /usr/local/gromacs/bin/g_covar_d -s average.pdb -f md0.mdcrd -o -v
I get the following error message.
Program g_covar_d, VERSION 4.5.5
Source code file: trxio.c, line: 870

Fatal error:
Not supported in read_first_frame: md0.mdcrd
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Thanks to Francesco, I know we should be able to readin AMBER's mdcrd files, did I do anything wrong here?  Could you mind to let me if I still did anything wrong here?
Best regards,

Hi Catherine,
you should install any gromacs *4.5.x*, and then you can use gromacs
with each trajectory supported by VMD because gromacs is able to use VMD plugin
perform trajectory reading.
1) Install the latest gromacs version
2) Install VMD
3) Set the variable VMD_PLUGIN_PATH to contain the complete path of the
molfile vmd directory.
   In my case, for example:  VMD_PLUGIN_PATH=/apps/vmd/1.9/**lib/vmd

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