cg_spica gen_gmxin [-pdb <pdbfile>] [-ndx <indexfile>] [-output <output>] [-pspica] [-em]


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 This program requires a GROMACS index file that can be generated by 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.


cg_spica gen_gmxin -pdb -em CGindex.ndx

table.xvg table_LJ124W_SOLW.xvg table_LJ96W_SOLW.xvg table_SOLW_SOLW.xvg npt.mdp minim.mdp

Optional args

-pdb <pdbfile> (conf.pdb)

System configuration file in PDB format

-ndx <indexfile> (CGindex.ndx)

GROMACS index file generated by 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