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SPICA: Surface Property fItting Coarse grAined model

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Parameter and topology files

SPICA

  • v1.0 -- DOWNLOAD
  • Version history
    [28.08.18] v1.0 -- First release.
  • Files:
    - spica_db.prm: Official SPICA force field file. This file can be read by setup_lammps
    - ./topology/*.top: Topology files for setup_lammps
    - spica_par.json: JSON formatted force field file for CG-it
    - ./topology/spica_top.json: Topology files for CG-it

Files for LAMMPS

Setup lammps

  • v1.0 -- DOWNLOAD
  • Version history
    [28.08.18] v1.0 -- First release (originally coded by Russell DeVane and modified by others)
  • How to use:
    - Untar the attached file and invoke "make" on linux shell. You will see the executable binary file, "setup_lammps".

    -
    Usage:
     setup_lammps <MOL_1.top> <N_MOL_1> [ <MOL_2.top> <N_MOL_2> . . . <MOL_n.top> < N_MOL_n> ] <param file> <coord file>
    • MOL_1.top, MOL_2.top, ... , MOL_n.top: Molecule topology file name
      (included in the force field file.)
    • N_MOL_1, N_MOL_2, N_MOL_n: Number of each molecule
    • param file: Force field parameter file: spica_db.prm (included in the force field file.)
    • coord file: Coordindate file name (in PDB format) 
    -
    Output files:
    • DATA.FILE: LAMMPS formatted coordinate file
    • PARM.FILE: LAMMPS formatted parameter file
  • Please refer to the tutorial for further details.

tSPICA

tSPICA Coefficents

tSPICA.py

  • v1.0 -- DOWNLOAD
  • How to use:
    -
    Usage:
     tSPICA.py <temperature> <pressure> <parameter_file> <coefficients_file>
    • temperature: Given in K
    • pressure: Given in MPa
    • parameter_file: Parameter file for LAMMPS
    • coefficients_file: tSPICA coefficient file
    -
    Output files:
    • t-parameter_file: updated parameter file for tSPICA
  • Please refer to the tutorial for further details here.

SPICA Force Field

Nagoya University