OpenMM OPS Engine

Primary Classes

Snapshot([statics, kinetics, is_reversed, …])

The standard snapshot for MD, based on statics and kinetics proxies.

MDSnapshot([velocities, coordinates, …])

A fast MD snapshot, which does not proxy the coordinates/velocities.

Engine

alias of openpathsampling.engines.openmm.engine.OpenMMEngine

engine.OpenMMEngine(topology, system, integrator)

OpenMM dynamics engine based on OpenMM system and integrator.

topology.MDTrajTopology(mdtraj_topology)

Utility functions

snapshot_from_pdb(pdb_file[, simple_topology])

Construct a Snapshot from the first frame in a pdb file without velocities

snapshot_from_testsystem(testsystem[, …])

Construct a Snapshot from openmm topology and state objects

trajectory_from_mdtraj(mdtrajectory[, …])

Construct a Trajectory object from an mdtraj.Trajectory object

empty_snapshot_from_openmm_topology(topology)

Return an empty snapshot from an openmm.Topology object

to_openmm_topology(obj)

Contruct an openmm.Topology file out of a Snapshot or Configuration object.