bgmol

----- WORK IN PROGRESS ------

A collection of OpenMM systems and data generated for those systems.

This package is an extension of the openmmtools.testsystems module with a twofold aim:

1. It contains a collection of OpenMM systems (with initial positions and topologies).
2. It provides infrastructure for sharing data (positions, forces, energies, velocities) generated for these systems.

Quickstart: Install

Make sure that you are in a conda environment that has OpenMM and mdtraj installed.

Clone the code

git clone [email protected]:noegroup/bgmol.git

And install

cd bgmol
python setup.py install

Quickstart: Example

from bgmol.datasets import Ala2Implicit300
dataset = Ala2Implicit300(download=True, read=True)

The dataset contains forces, energies and coordinates it also holds a reference to the system that defines the potential energy function.

openmmsystem = dataset.system

The system is an OpenMMSystem object, it provides access to the simtk.openmm.system instance, the topology, and a set of initial coordinates. For example, we can run an OpenMM simulation as follows

from simtk.openmm.app import Simulation, LangevinIntegrator
integrator = LangevinIntegrator(dataset.temperature, 1, 0.001)
simulation = Simulation(openmmsystem.topology, openmmsystem.system, integrator)
simulation.context.setPositions(openmmsystem.positions)
simulation.step(10)

The dataset contains coordinates (xyz), forces, and energies.

dataset.energies

Adding Systems to the Repository

The preferred way to add systems is by adding a subclass of OpenMMSystem to the bgmol.systems module, see examples therein.

Adding Samples to the Repository

TBD

Copyright

Copyright (c) 2020, noegroup

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.2.