setup_lmp¶
Usage¶
cg_spica setup_lmp <topfile 1> <nmol 1> [<topfile 2> <nmol 2> ... <topfile n> <nmol n>]
<paramfile> <coordfile>
Description¶
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 webparamfile: SPICA parameter file, distributed at SPICA webcoordfile: 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:
DATA.FILE: LAMMPS DATA filePARM.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.
Example¶
cg_spica setup_lmp DOPC.top 128 WAT.top 1408 spica_db.prm dopc.cg.pdb
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