mstk 0.3.3.dev11

Molecular simulation toolkit

mstk

A toolkit to make molecular simulation less painful

Capabilities

• Assign atom types and force field parameters based on local chemical environment
• Generate input files for simulation engines like LAMMPS, GROMACS, NAMD, OpenMM
• Support Drude polarizable model, coarse-grained model, virtual site, linear angle...
• Read/write common topology files (LAMMPS, PSF, PDB, ZMAT etc...)
• Read/write common trajectory files (LAMMPS, GRO, DCD, XTC, etc...)
• Access local and remote job schedulers like Slurm, Torque

Examples

The following code builds a liquid mixture of 100 benzene and 1000 water molecules, ready for simulation.

from mstk.topology import Molecule, Topology
from mstk.forcefield import ForceField, typer_primitive
from mstk.simsys import System
from mstk.wrapper import Packmol

# Create molecule structures from SMILES
benzene = Molecule.from_smiles('c1ccccc1')
water = Molecule.from_smiles('O')
top = Topology([benzene, water])

# Assign atom type as defined in `data/forcefield/primitive.zft`
typer_primitive.type(top)

# Build a bulk liquid simulation box with Packmol
packmol = Packmol('/path/to/packmol')
top.cell.set_box([4.0, 4.0, 4.0])
top.scale_with_packmol([100, 1000], packmol=packmol)

# Assign force field as defined in `data/forcefield/primitive.zff`
ff = ForceField.open('primitive.zff')
ff.assign_charge(top)
system = System(top, ff)

# generate input files for LAMMPS, GROMACS and NAMD
system.export_lammps()
system.export_gromacs()
system.export_namd()

# generate an OpenMM system
omm_sys = system.to_omm_system()

Documentation

https://mstk.readthedocs.io/en/latest/index.html

TODO

• Take bond order into consideration for force field assignment
• Re-organize algorithms scattered in topology and analyzer modules