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.
From source
python setup.py install
With conda
conda install -c omnia openmmmcmc-dev
Classes to cache a maintain a consistent state of the simulation.
ThermodynamicState
: Represent and manipulate the thermodynamic state of OpenMMSystem
s andContext
s.SamplerState
: Represent and cache the state of the simulation that changes when theSystem
is integrated.CompoundThermodynamicState
: Extend theThermodynamicState
to handle parameters other than temperature and pressure through the implementations of theIComposableState
abstract class.
An implementation of an MCMCMove
encodes how to propagate an OpenMM System
to generate a new sample. Different MCMCMove
s 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.