The problem I'm referring to is here:
Subject: Installed Gromacs but generate contact map using g_mdmat (Gromacs) still failed
Date: Mon, 12 Mar 2012 08:57:11 +1200
We've just successfully installed Gromacs on Ubuntu Linux (Virtual Machine) but the problem is when running g_mdmat from Gromacs package by the following command
g_mdmat -f 2p31.pdb -s 2p31.pdb -mean contact-map.xpm
The result gives me 'no command found'
Perhaps we haven't connected Gromacs to PyMOL to make this work?