CHARMM: The biomolecular simulation program

A review. CHARMM (Chem. at HARvard Mol. Mechanics) is a highly versatile and widely used mol. simulation program. It has been developed over the last three decades with a primary focus on mols. of biol. interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small mol. ligands, as they occur in soln., crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, mol. minimization, dynamics, and anal. techniques, and model-​building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-​particle systems. Calcns. with CHARMM can be performed using a no. of different energy functions and models, from mixed quantum mech.-​mol. mech. force fields, to all-​atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.