.. _g_mmpbsa:

g_mmpbsa
========

De acordo com a `página do g_mmpbsa <https://rashmikumari.github.io/g_mmpbsa/>`_,
"*g_mmpbsa is a console application which is executed from terminal/console by
command options similar to other GROMACS module. All the input options should
be provided on command line depending on the type of calculation. To calculate
for single atomic group (e.g. only protein, only ligand, only specific region
of protein etc.) one group is required to choose from index file, whereas for
complex (e.g. protein-ligand, protein-protein etc.) two separate group is
required to choose from index file.*".


Versões disponíveis
-------------------

* g_mmpbsa/gromacs-5.1


Submissão de Jobs em Serial
---------------------------

Crie um arquivo chamado, por exemplo, *submit_serial_jobs.sh*.

.. code-block:: bash

   #!/bin/bash
   #SBATCH -t 24:00:00

   export INPUT="traj.xtc topol.tpr mmpbsa.mdp polar.xvg apolar.xvg contrib_MM.dat contrib_pol.dat contrib_apol.dat"
   export OUTPUT="*"

   module load g_mmpbsa/gromacs-5.1

   job-nanny g_mmpbsa -f traj.xtc -s topol.tpr \
                      -i mmpbsa.mdp -n index.ndx -pbsa \
                      -mm energy_MM.xvg -pol polar.xvg \
                      -apol apolar.xvg -decomp \
                      -mmcon contrib_MM.dat -pcon contrib_pol.dat \
                      -apcon contrib_apol.dat

Para submeter o processo, basta usar o comando:

.. code-block:: bash

   sbatch submit_serial_jobs.sh


Referências
-----------

Para informações adicionais sobre o software, consulte a `documentação do g_mmpbsa <https://rashmikumari.github.io/g_mmpbsa/How-to-Run.html>`_.