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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 tara


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.