/openmmtools

Test systems for OpenMM

Primary LanguagePython

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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 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.