cg_spica setup_lmp <topfile 1> <nmol 1> [<topfile 2> <nmol 2> ... <topfile n> <nmol n>]
                   <paramfile> <coordfile>


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

  • topfile: SPICA topology file, distributed at SPICA web

  • paramfile: SPICA parameter file, distributed at SPICA web

  • coordfile: CG configuration file in PDB format

The topfile can be generated with json2top, or ENM (for proteins only) commands. For more information on these, see json2top and ENM. The nmol is the number of topfile molecules included in your 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 in the PDB file.

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


  • PARM.FILE: Interaction parameter file that should be read when executing LAMMPS CG-MD.

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

DATA.FILE and PARM.FILE are required to run LAMMPS CG-MD with SPICA FF. Specify them in the LAMMPS simulation input file to start the simulation. Input examples are distributed in lipid membrane tutorial on SPICA web. Although out.psf is not needed to run CG-MD, it will be useful to visualization and analysis of the system because it has all the topology information on the bonds and angles of molecules included in the system.


cg_spica setup_lmp 128 1408 spica_db.prm spica_db.prm


Positional args

topfile <topology>

topology file of a molecule

nmol <int>

number of molecules

paramfile <parameter>

SPICA force field parameter file

coordfile <.pdb>

CG configuration file