mstk 0.4.0

Molecular simulation toolkit

mstk

A toolkit to make molecular simulation less painful

mstk is a Python toolkit designed to streamline the setup and management of molecular simulations, particularly geared towards non-biological applications in material science and chemical engineering. It simplifies atom typing, force field parameter assignment, and input file generation for major simulation engines.

Features

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

Installation

conda install -c conda-forge numpy pandas rdkit openmm chemfiles packmol pymbar-core
pip install mstk

Quick Example

Example 1 Build 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
from mstk.simsys import System
from mstk.wrapper import Packmol

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

# Assign atom types as defined in `data/forcefield/primitive.smt`
typer = Typer.open('primitive.smt')
typer.type(top)

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

# Assign force field parameters 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()

Important Note: The primitive atom typing and force field used above are for demonstration purpose only and are not well optimized for production use. For reliable simulation, please prepare you own smt and zff files or get them from a validated source.

Example 2 Calculate the hydration free energy of benzene in water

• 2.1 Build a system containing 1 benzene in 1000 water, following the above example

• 2.2 Use the mstk sfe run command to perform alchemical simulation under different lambda windows

mstk sfe run -p _namd-top.psf -c _gmx-conf.gro -f primitive.zff --molid 0 -w %WINDOW% --nwindow 16

Run at 16 different windows by change %WINDOW% from 0 to 15. A series of dU values will be saved in dU_%WINDOW%.csv

• 2.3 Use the mstk sfe mbar command to analyse free energy change

mstk sfe mbar *.csv

Documentation

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

TODO

• Refactor algorithms across topology and analyzer modules
• Separate ommhelper module into its own package
• Remove analyzer module
• Revise the implementation of Drude polarization and virtual sites