Detailed Description

Classes that implement free energy perturbation theory and replica exchange.

This module contains the Perturbation abstract base class and its concrete subclasses. Subclasses of Perturbation describes the dependence of the Boltzmann weight upon a parameter. The parameter may be either a parameter in the Hamiltonian (i.e., and interaction strength) or the inverse temperature beta = 1/(kT) that multiplies the Hamiltonian. When used in parallel mode, a Perturbation may be used to assign different values of a perturbation parameter to different processors.

This module also contains the ReplicaMove class, which implements a replica exchange or parallel tempering simulation algorithm. In replica exchange, different processors simulate systems with different values of the perturbation parameter, and occasionally exchange configurations. The ReplicaMove algorithm is always used in conjunction with a concrete subclass of Perturbation, which defines how the Botzmann weight depends upon a particular tempering parameter.

Classes
class	McMd::McEnergyPerturbation
	A Perturbation with a variable inverse temperature. More...

class	McMd::McExternalPerturbation< Interaction >
	A Perturbation in the external potential external parameter. More...

class	McMd::McPairExternalPerturbation< PairInteraction, ExternalInteraction >
	A Perturbation in the pair interaction epsilon(0,1) for any pair potential supporting setEpsilon() and in the external parameter for any external potential supporting setExternalParameter(). More...

class	McMd::McPairPerturbation< Interaction >
	A Perturbation in the pair interaction epsilon(0,1) for any pair potential supporting setEpsilon(). More...

class	McMd::McPerturbationFactory
	Default Factory for subclasses of Perturbation. More...

class	McMd::Perturbation
	Model of parameter dependence in a free energy perturbation theory. More...

class	McMd::ReplicaMove
	Replica exchange Monte Carlo move using Gibbs sampling. More...