OpenMM MCMC

A general Markov chain Monte Carlo framework for OpenMM.

WARNING: This is a work in progress. These functionalities will be moved shortly to the more comprehensive package OpenMMTools.

Installation

From source

python setup.py install

With conda

conda install -c omnia openmmmcmc-dev

States

Classes to cache a 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.

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.