gen_gmxin
===============
Usage   
--------
.. parsed-literal::

    cg_spica gen_gmxin [:strong:`-pdb` :emphasis:`<pdbfile>`] [:strong:`-ndx` :emphasis:`<indexfile>`] [:strong:`-output` :emphasis:`<output>`] [:strong:`-pspica`] [:strong:`-em`]

Description
-----------
``gen_gmxin`` generates GROMACS mdp and table files for MD simulations with the NPT ensemble using SPICA or pSPICA.
The usage of GROMACS with SPICA can be found on https://github.com/SPICA-group/gromacs-spica.
This program requires a GROMACS index file that can be generated by :doc:`setup_gmx <setup_gmx>`, as well as a system configuartion file in PDB format.
The table files (``table.xvg`` and ``table_*_*.xvg``) for nonbonded tabulated potentials are generated based on the input index file.
The index groups in the index file include:

    * SOLW : CG water and ions
    * LJ124W : CG sites interaction with water through LJ12-4 potential
    * LJ96W : CG sites interacting with water through LJ9-6 potential
    * PSOLW : polar CG water and ions (for pSPICA)

The table files needed for GROMACS simulations with SPICA or pSPICA are properly generated for the index groups through this program.
See `gromacs-spica`_ repository for the detail of GROMACS usage with SPICA.

The generated mdp file by this command is useful to start CG-MDs using SPICA or pSPICA.
Before running your CG-MD, please check the simulation settings in the file yourself.

.. _gromacs-spica: https://github.com/SPICA-group/gromacs-spica

Example
-------
.. code-block:: bash

    cg_spica gen_gmxin -pdb prot_memb.cg.pdb -em

:download:`prot_memb.cg.pdb <data/setup_gmx_prot/prot_memb.cg.pdb>`  
:download:`CGindex.ndx <data/setup_gmx_prot/CGindex.ndx>`  

:download:`table.xvg <data/setup_gmx_prot/table.xvg>`  
:download:`table_LJ124W_SOLW.xvg <data/setup_gmx_prot/table_LJ124W_SOLW.xvg>`  
:download:`table_LJ96W_SOLW.xvg <data/setup_gmx_prot/table_LJ96W_SOLW.xvg>`  
:download:`table_SOLW_SOLW.xvg <data/setup_gmx_prot/table_SOLW_SOLW.xvg>`  
:download:`npt.mdp <data/setup_gmx_prot/npt.mdp>`  
:download:`minim.mdp <data/setup_gmx_prot/minim.mdp>`  

Optional args
---------------

``-pdb`` <pdbfile> (conf.pdb)
    System configuration file in PDB format
``-ndx`` <indexfile> (CGindex.ndx)
    GROMACS index file generated by :doc:`setup_gmx <setup_gmx>`
``-output`` <mdpfile> (npt.mdp)
    Output GROMACS mdp file name
``-pspica`` (off)
    Generate a mdp file for pSPICA
``-em`` (off)
    Generate an additional mdp file for energy minimization