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CHARMM: The biomolecular simulation program
B. R. Brooks, C. L. Brooks III, A. D. Mackerell Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, Martin Karplus

CHARMM-GUI: A web-based graphical user interface for CHARMM
Sunhwan Jo, Taehoon Kim, Vidyashankara G. Iyer, Wonpil Im

A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations
Field MJ, Bash PA, Karplus M. A

Harmonic analysis of large systems. I. Methodology
Bernard R. Brooks, Dušanka Janežič, Martin Karplus

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
Christian Bartels, Martin Karplus

Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex
Amedeo Caflisch, Stefan Fischer, Martin Karplus

Monte Carlo simulations of biomolecules: The MC module in CHARMM
Jie Hu, Ao Ma, Aaron R. Dinner

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations
H. Lee Woodcock III, Milan Hodošček, Andrew T. B. Gilbert, Peter M. W. Gill, Henry F. Schaefer III, Bernard R. Brooks

Empirical energy functions for energy minimization and dynamics of nucleic acids
Lennart Nilsson, Martin Karplus

Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
Alexander D. Mackerell Jr., Michael Feig, Charles L. Brooks III

Additive empirical force field for hexopyranose monosaccharides
Olgun Guvench, Shannon N. Greene, Ganesh Kamath, John W. Brady, Richard M. Venable, Richard W. Pastor, Alexander D. Mackerell Jr

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, A. D. Mackerell Jr.

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
Sandeep Patel, Charles L. Brooks III

CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
Sandeep Patel, Alexander D. Mackerell Jr., Charles L. Brooks III