Introduction

The GROMACS software on maya is available under

[araim1@maya-usr1 ~]$ ls /usr/cluster/gromacs/4.6.5/
bin  include  lib  share
[araim1@maya-usr1 ~]$

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

[araim1@maya-usr1 ~]$ 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@maya-usr1 ~]$

Load the gromacs module so that they are also in your path and they can be used without typing the full path.

[araim1@maya-usr1 user-resources]$ module load gromacs/4.6.5
[araim1@maya-usr1 user-resources]$ module list
Currently Loaded Modulefiles:
  1) gcc/4.8.1                                       5) mvapich2/intel/composer_xe_2013_sp1.1.106/1.9
  2) slurm/14.03.6                                   6) texlive/2014
  3) matlab/r2014a                                   7) gromacs/4.6.5
  4) intel/2013_sp1.1.106

[araim1@maya-usr1 ~]$ g_select
                         :-)  G  R  O  M  A  C  S  (-:

           Glycine aRginine prOline Methionine Alanine Cystine Serine

                            :-)  VERSION 4.6.5  (-:
...

See the GROMACS website for information on using the software.