setup_gmx

Usage

cg_spica setup_gmx <topfile 1> <nmol 1> [<topfile 2> <nmol 2> ... <topfile n> <nmol n>] <paramfile> [<coordinate>] [-prot]

Description

setup_gmx generates simulation input files for CG-MD with SPICA using GROMACS. This program requires the following files as inputs:

• topfile: SPICA topology file, distributed at SPICA web

• paramfile: SPICA parameter file, distributed at SPICA web

The topfile can be generated with the json2top or ENM (for proteins only) commands. For more details, see json2top and ENM. The nmol is the number of topfile molecules in the system. It is sensitive to the order of arguments, so the molecule topology and number should be given in the same order as given in the prepared configuration file.

Unlike the setup_lmp command, this program does not normally require a pdb configuration file, because it generates input files needed only to execute the gmx grompp command in GROMACS.

Use the -prot option is used to set up systems containing proteins. This is because SPICA takes protein equilibrium angle values from the initial configuration. In this case, a configuration file in PDB format must be specified as the last argument of the program.

Running the program with the appropriate input files yields the following outputs:

• toppar/

  • SPICA.itp: SPICA force field parameter

  • {molecule}.itp: Included topology files for each molecule.

• topol.top: System topology file including SPICA.itp and {molecule}.itp

• CGindex.ndx: Atom index file of a target system

• out.psf: Topology file of a target system in PSF format

NOTE

The standard GROMACS package does NOT support the SPICA angle or nonbonded interactions. To use SPICA with GROMACS, the package must be modified with the patch file for the angular interaction in gromacs-spica repository, and the tabulated potentials for the nonbonded interaction must be applied.

Example

cg_spica setup_gmx DOPC.top 128 WAT.top 1408 spica_db.prm

DOPC.top WAT.top spica_db.prm

topol.top SPICA.itp DOPC.itp WAT.itp CGindex.ndx out.psf

cg_spica setup_gmx 1d6x.cg.top 1 DOPC.top 128 WAT.top 2134 CLA.top 4 spica_db.prm prot_memb.cg.pdb -prot

1d6x.cg.top DOPC.top WAT.top CLA.top spica_db.prm prot_memb.cg.pdb

topol.top SPICA.itp 1d6x.cg.itp DOPC.itp WAT.itp CLA.itp CGindex.ndx out.psf

Positional args

topfile <topology>

topology file of a molecule

nmol <int>

number of molecules

paramfile <parameter>

SPICA force field parameter file

Optional args

-prot (off)

Read a pdb configuration file to extract reference angle for protein models

coordfile <.pdb>

CG configuration file, required when the -prot option is set