SPICA: Surface Property fItting Coarse grAined model

TutorialpSPICA

pSPICA

pSPICA is a CG FF designed with a polar CG water model. The CG modeling method of pSPICA is the same as the SPICA FF. The LJ12-5 function is adopted to simultaneously reproduce the experimental density, surface tension, and dielectric permittivity of water (A brief summary of the model is given here, and the publication with full details here ). For simulations with LAMMPS there is already a script to use the LJ12-5 function by changing the LAMMPS parameter file generated by setup_lammps. The tutorial for generating LAMMPS parameter files can be found here. There is another script to change the uncharged CG water of the SPICA FF to the polar CG water of pSPICA.

download pSPICA script to modify lammps parameter files
download pSPICA script to replace CG water
download Database file

convert_PARM.py useage:


$ convert_PARM.py input_Parameter_file output_Parameter_file

input/output_Parameter_file = Path to input/output parameter_file. File in LAMMPS format

WAT2PWAT.py useage:


$ WAT2PWAT.py input_Configuration_file output_Configuration_file

input/output_Configuration_file = Path to input/output configuration_file. File in PDB format

Example:

Files for tutorial: Input pSPICA Parameter fileOutput pSPICA parameter file

A simulation of a lipid membrane system composed of 128 DMPC lipids and 1152 polar CG water particles. Here we will start the simulation from an initial configuration obtained by using the SPICA FF.
First, we replace the uncharged water of the SPICA FF in the initial configuration with the polar water of pSPICA.
The command is:
$ WAT2PWAT.py spica_conf.pdb pspica_conf.pdb

Next we run the setup_lammps script for the initial configuration that was generated (The usage of the script can be found here).
$ setup_lammps PDMPC.top 128 PWAT.top 1152 pSPICA_lipid.prm pspica_conf.pdb

After that, we modify the obtained PARM.FILE to use tabulated potential in LAMMPS as follows:
$ convert_PARM.py PARM.FILE pPARM.FILE

The header of pPARM.FILE should look like:

# Generated by setup_lammps

pair_style hybrid/overlay lj/sdk 15.0 coul/long 15.0 table linear 2999
bond_style harmonic
angle_style hybrid sdk harmonic
...

pair_coeff 1 1 lj/sdk lj9_6 0.5650 5.4500 # NC NC
pair_coeff 1 1 coul/long # NC NC
...
pair_coeff 8 8 table 12_5ww.t TABLE 15.0 # WO WO
pair_coeff 8 8 coul/long # WO WO
...

Note: 12_5xy.t is a file containing tabulated energy and force values of the LJ12-5 interaction between x and y (x,y = w:water, s:sodium, or c:chloride).

For LAMMPS input files to perform the simulation with pSPICA (check an attached file, pSPICA_example/in.npt), we have to be careful to include two mandatory commands, "dielectric" and "fix shake".
The two commands in the input should look like:

...
dielectric 3.2
...

...
fix Fix0 all shake 1.0e-6 25 0 b 9
...

Note: The b of the "fix shake" command lists the bond types that will be constrained.

The LAMMPS simulation can now be run using DATA.FILE, pPARM.FILE with 12_5xy.t, and the input ( tutorial for SPICA simulations in LAMMPS).

SPICA Force Field

Research Institute for Interdisciplinary Science (RIIS)
Okayama University