openmm-mdanalysis-reporter 0.1

MDAnalysis based reporter for OpenMM

openmm-mdanalysis-reporter

Latest release
Status
Community

MDAnalysis based reporter for OpenMM

openmm-mdanalysis-reporter is bound by a Code of Conduct.

Currently a WIP but it should work

This is an OpenMM Reporter class that uses MDAnalysis for output. This means it can use any format supported by MDAnalysis. It also supports MDAnalysis selection strings.

The reporter is called MDAReporter, once this package is installed it can be imported as:

from mdareporter import MDAReporter

Installation

Pip:

pip install git+https://github.com/sef43/openmm-mdanalysis-reporter

From source:

git clone https://github.com/sef43/openmm-mdanalysis-reporter.git
cd openmm-mdanalysis-reporter
pip install .

Usage

It is used like the existing OpenMM reporters, where the file format is read from the suffix of the output file by MDAnalysis, e.g. to output in XYZ format:

from mdareporter import MDAReporter

...

simulation.reporters.append(MDAReporter('traj.xyz',100))
...

Additionally it supports the MDAnalysis selection syntax

# using MDAnalysis selection string to output just Carbon atoms

simulation.reporters.append(MDAReporter('traj.xyz',100, selection='name C'))

Example

Full example of using MDAReporter to output just the protein (script and data file in cd example):

from openmm.app import *
from openmm import *
from openmm.unit import *
from sys import stdout
from mdareporter import MDAReporter


pdb = PDBFile('villin.pdb')
forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME,
        nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
simulation = Simulation(pdb.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.minimizeEnergy(maxIterations=100)

# output just protein in xyz format
simulation.reporters.append(MDAReporter('traj.xyz',100, enforcePeriodicBox=False, selection="protein"))

simulation.reporters.append(StateDataReporter(stdout, 100, step=True,
        potentialEnergy=True, temperature=True))

simulation.step(1000)
    

Testing

testsuite can be run using pytest

cd mdareporter/tests
pytest

or

pytest --pyargs mdareporter.tests   

Benchmarks

A benchmarking script which writes trajectory snapshots every 10 steps for 1000 steps can be found at example/benchmark.py

The output on a M2 Macbook is:

OpenMM PDBReporter time =  7.989748208987294 s
OpenMM DCDReporter time =  5.6639587499958 s
MDAReporter format DCD time =  3.5682871250028256 s
MDAReporter format NCDF time =  3.609358207992045 s
MDAReporter format PDB time =  11.491382707987214 s
MDAReporter format TRR time =  4.7894440419913735 s
MDAReporter format XTC time =  4.086603666975861 s
MDAReporter format XYZ time =  5.835725833981996 s

Excluding MDAReporter using PDB format the MDAReporter formats are all as fast, or faster than the OpenMM formats.

Acknowledgements

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using openmm-mdanalysis-reporter in published work.