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Various Python tools for OpenMM

Integrators

This repository contains a number of additional integrators for OpenMM in openmmtools.integrators, including

  • MTSIntegrator - a multiple timestep integrator
  • DummyIntegrator - a "dummy" integrator that does not update positions
  • GradientDescentMinimizationIntegrator - a simple gradient descent minimizer (without line search)
  • VelocityVerletIntegrator - a velocity Verlet integrator
  • AndersenVelocityVerletIntegrator - a velocity Verlet integrator with Andersen thermostat using per-particle collisions
  • MetropolisMonteCarloIntegrator - a Metropolis Monte Carlo integrator that uses Gaussian displacement trials
  • HMCIntegrator - a hybrid Monte Carlo (HMC) integrator
  • GHMCIntegrator - a generalized hybrid Monte Carlo (GHMC) integrator
  • VVVRIntegrator - a velocity Verlet with velocity randomization (VVVR) integrator

Test system suite

The openmmtools.testsystems module contains a large suite of test systems---including many with simple exactly-computable properties---that can be used to test molecular simulation algorithms

Monte Carlo moves

An implementation of an MCMCMove encodes how to propagate an OpenMM System to generate a new sample. Different MCMCMoves can be combined for more advanced schemes.

  • LangevinDynamicsMove: Langevin dynamics segment as a (pseudo) Monte Carlo move.
  • HMCMove: Assigns velocities from the Maxwell-Boltzmann distribution and propagate through velocity Verlet steps.
  • GHMCMove: Generalized hybrid Monte Carlo Markov chain Monte Carlo.
  • MonteCarloBarostatMove: Attempts to update the box volume using Monte Carlo updates.
  • SequenceMove: Combine multiple MCMCMoves to apply in sequence at each iteration.
  • WeightedMove: At each iteration, select one MCMCMoves to apply from a set with given probability.

States

The module openmmtools.states contains classes to maintain a consistent state of the simulation.

  • ThermodynamicState: Represent and manipulate the thermodynamic state of OpenMM Systems and Contexts.
  • SamplerState: Represent and cache the state of the simulation that changes when the System is integrated.
  • CompoundThermodynamicState: Extend the ThermodynamicState to handle parameters other than temperature and pressure through the implementations of the IComposableState abstract class.

Cache

The module openmmtools.cache implements a shared LRU cache for Context objects that tries to minimize the number of Context in memory at the same time.

  • LRUCache: A simple LRU cache with a dictionary-like interface. It supports a maximum capacity and expiration.
  • ContextCache: A LRU cache for OpenMM Context objects.
  • global_context_cache: A shared ContextCache that minimizes the number of Context creations when employing MCMCMoves.

OpenMM testing scripts

scripts/ contains a script that may be useful in testing your OpenMM installation is installed:

  • test-openmm-platforms will test the various platforms available to OpenMM to ensure that all systems in openmmtools.testsystems give consistent potential energies. If differences in energies in excess of ENERGY_TOLERANCE (default: 0.06 kcal/mol) are detected, these systems will be serialized to XML for further debugging.

This is installed onto the command line when the repository is installed.