McMd namespace

Detailed Description

McMd namespace (single-processor MC and MD)

Modules
	Analyzers
	Classes that implement data analysis or output operations.
	Chemical Structure
	Classes that describe atoms, molecules, and groups of atoms.
	Commands
	Operations that can be invoked from the command script.
	Configuration File IO
	A ConfigIo object can read and write the configuration file for a System.
	Generators
	Classes that generate random initial configurations.
	Monte Carlo Moves
	This module contains all McMove (Monte Carlo Move) classes.
	Molecular Dynamics Integrators
	Molecular dynamics integration algorithms.
	Nonbonded Neighbors
	Classes used to keep track of nonbonded neighbors.
	Free Energy Perturbation
	Classes that implement free energy perturbation theory and replica exchange.
	Potential Energies
	Classes used by a System calculate potential energies.
	Managers
	A Manager is a container for objects with a common base class.
	Simulations
	A Simulation object represents a complete simulation.
	Systems
	A System is a set of interacting Molecules enclosed by a Boundary.
	Trajectory Readers
	Classes that can read trajectory files for analysis.