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UMBC High Performance Computing Facility
Please note that this page is under construction. We are documenting the 240-node cluster maya that will be available after Summer 2014. Currently, the 84-node cluster tara still operates independently, until it becomes part of maya at the end of Summer 2014. Please see the 2013 Resources Pages under the Resources tab for tara information.
How to run GROMACS on maya

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.