gen_gmxin

Usage

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

Example

cg_spica gen_gmxin -pdb prot_memb.cg.pdb -em

prot_memb.cg.pdb 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