mstk 0.3.8

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

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, ZftTyper
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 = ZftTyper('primitive.zft')
typer.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 OpenMM system and topology
omm_sys = system.to_omm_system()
omm_top = top.to_omm_topology()

Documentation

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

TODO

• Take bond order into consideration for force field assignment
• Add frozen marker in ZFF and ZFP for force field optimization
• Re-organize algorithms scattered in topology and analyzer modules

Known issue

mstk use chemfiles to write XTC trajectory. However, lastest chemfiles fails writing binary trajectory format under WSL 1. If you are using WSL 1, please install chemfiles 0.10.2

conda install chemfiles-lib=0.10.2 chemfiles-python=0.10.2