CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular dynamics and mechanics. It performs standard molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation and periodic images. CHARMM can be used for energy minimization, normal modes and crystal optimizations as well. The potential energy functions available for use with CHARMM have been extensively parameterized for simulations of proteins, nucleic acids and lipids. Free energy methods for chemical and conformational free energy calculations are also fully developed and available in CHARMM. Many other novel tools have been developed and are available in CHARMM, these include: replicas (multiple copies); many types of restraints and constraints, including fixed atoms, atomic, NOE, dihedral and internal coordinate restraints and generalized SHAKE for bonds and arbitrary internal co ordinates; minimium energy path following and transition state optimization; etc.