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 algorith,s

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.