lmpanlys

Tools for LAMMPS.

Installation

Clone the repository

  1. git clone https://github.com/vt87/lmpanlys.git

Add the following in ~/.bashrc

  2. export PYTHONPATH="{PATH}/lmpanlys/src:$PYTHONPATH"

PATH is where git directory is cloned.

Source the bashrc using the following command

  3. source ~/.bashrc

Example

cd ~/test

git clone https://github.com/vt87/lmpanlys.git

export PYTHONPATH="~/test/lmpanlys/src:$PYTHONPATH"

source ~/.bashrc

Usage

Obtaining the pair coefficients in LAMMPS format for Martini by reading GROMACS Martini database file

Create martini.inp file containing lammps type and corresponding Martini label separated by at least one space.

Example

1 C5

2 TN1a

3 P1

NOTE : Different lines for different types.

Run the following script on Python

from paircoeffs_martini import paircoeffs_martini
m = paircoeffs_martini(fname = "martini.inp",
                       database = $GROMACS_DATABASE_FILE$)

GROMACS_DATABASE_FILE is the location of Martini 3.0.0 database file in your computer.

For reference, file is provided in utils/databases/martini_v3.0.0.itp

Output of the script will generate paircoeffs.txt in LAMMPS format. Example below

# MARTINI force field
# The bead id and its martini label are as follows
# 1 C5
# 2 TN1a
# 3 P1
pair_style lj/gromacs 9.0 12.0
pair_coeff 1 1 0.810229 4.700000 9.0 12.0
pair_coeff 1 2 0.552103 3.950000 9.0 12.0
pair_coeff 1 3 0.733748 4.700000 9.0 12.0
pair_coeff 2 2 0.360899 3.400000 9.0 12.0
pair_coeff 2 3 0.552103 3.950000 9.0 12.0
pair_coeff 3 3 0.927342 4.700000 9.0 12.0

NOTE: lj/gromacs is part of the EXTRA-PAIR package

Additional options

Script with additonal options

from paircoeffs_martini import paircoeffs_martini
m = paircoeffs_martini(fname = "martini.inp",
                       database = "../utils/database_martini/martini_v3.0.0.itp",
                       cutoff = 1.2,
                       inner_cutoff = 0.9,
                       fftype = "lj/gromacs",
                       ofile = "paircoeffs.txt")

fname : Name of input file

database : Location of Gromacs Martini database file

cutoff : LJ cutoff (in nanometers)

inner_cutoff : LJ inner cutoff (in nanometers) . Used in lj/gromacs

fftype : Type of potential. Only two options are allowed; lj/cut or lj/gromacs

ofile : Name of output file

Testing

Go to tests folder. Run martini_test.py.

Bug me if you find bugs