Introduction

The GROMACS software on tara is available under

[araim1@tara-fe1 ~]$ ls /usr/cluster/gromacs/4.0.7/
bin  include  lib  share
[araim1@tara-fe1 ~]$

The executables are in the bin subdirectory and have a "g_" prefix.

[araim1@tara-fe1 ~]$ ls /usr/cluster/gromacs/4.0.7/bin
completion.bash       g_eneconv              g_mdrun              g_saltbr
completion.csh        g_eneconv_d            g_mdrun_d            g_saltbr_d
completion.zsh        g_eneconv_d_debug      g_mdrun_d_debug      g_saltbr_d_debug
g_anadock             g_eneconv_debug        g_mdrun_debug        g_saltbr_debug
...
[araim1@tara-fe1 ~]$

They are also in your PATH, so you can use them without typing the full path.

[araim1@tara-fe1 ~]$ g_pdb2gmx
                         :-)  G  R  O  M  A  C  S  (-:

               Giant Rising Ordinary Mutants for A Clerical Setup

                            :-)  VERSION 4.0.7  (-:
...

See the GROMACS website for information on using the software.