CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates and small molecule ligands, as they occur in solution, 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, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. In addition, the CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical 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 paper provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM paper in 1983.

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The optical spectra of the reaction center (RC) from Rhodopseudomonas viridis including absorption, polarized light absorption, and circular dichroism are simulated by employing an effective Hamiltonian of a vibronically coupled exciton manifold, which explicitly includes vibronic coupling to intraand intermolecular vibrational modes. Thermally averaged Green's function matrix elements of the RC model Hamiltonian are computed by utilizing an approximate matrix continued fraction expansion, from which all single-photon optical line shapes are well-reproduced at various temperatures. The results support an analysis of photochemical hole-burning experiments (see the following paper) using an identical effective Hamiltonian.

Presented are parameters for mono-, di-, and trivalent cations compatible with the CHARMM additive force field and the TIP3P water model. Thermodynamic perturbation molecular dynamics simulations were performed for the cations located at the center of a TIP3P water sphere under a solvent boundary potential. A series of perturbations generated free energies of hydration indexed by the two Lennard-Jones parameters, ε and R(min). Interpolating the experimental free energies of hydration showed that multiple combinations of ε and R(min) values reproduced the free energies of hydration for each ion. To overcome this nonunique parameter problem, the hydration shell model in combination with an empirical scaling parameter was applied to assign values for each ion. R(min) values were then identified via interpolation of the calculated free energies of hydration. The presented parameters are anticipated to be of utility for simulations of ions, including ions complexed to proteins.

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The pseudospectral (PS) method for self-consistent-field calculations is extended for use in generalized valence-bond calculations and is used to calculate singlet-triplet excitation energies in methylene, silylene, and ethylene molecules and bond dissociation and twisting energies in ethylene. We find that the PS calculations lead to an accuracy in total energies of <0.1 kcallmol and excitation energies to <0.01 kcallmol for all systems. With effective core potentials on Si, we find greatly improved accuracy for PS.

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