CHARMM dynamics

Bernhard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, and Martin Karplus. CHARMM A program for macro-molecular energy, minimization, and dynamics calculations. J. Comp. Chem., 4(2) 187-217, 1983. 

Watanabe, M., Karplus, M. Dynamics of Molecules with Internal Degrees of Freedom by Multiple Time-Step Methods. J. Chem. Phys. 99 (1995) 8063-8074 Figueirido, F., Levy, R. M., Zhou, R., Berne, B. J. Large Scale Simulation of Macromolecules in Solution Combining the Periodic Fast Multiple Method with Multiple Time Step Integrators. J. Chem. Phys. 106 (1997) 9835-9849 Derreumaux, P., Zhang, G., Schlick, T, Brooks, B.R. A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications. J. Comp. Chem. 15 (1994) 532-555... 

Brooks, B.R. Bruccoleri, R.E. Olafson, B.D. States, D.J. Swaminathan, S. Karpins, M. CHARMM A program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 187-217, 1983. 

AMBER, GROMOS, QUANTA/CHARMm molecular dynamics (see text)... 

Performance. The total time for 500 steps of dynamics and 25 nonbond updates for the standard CHARMM benchmark (Brunger, A. T., Harvard University, personal communication, 1985.), a B-DNA eleven-mer duplex with 706 atoms and a 11.5 angstrom nonbond cutoff (77000 nonbond pairs) is found in Table II. 

Drude oscillators, Fluctuating charge, Molecular dynamics, CHARMM... 

Patel S, Mackerell AD, Brooks CL (2004) CHARMM fluctuating charge force field for proteins II -Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem 25(12) 1504-1514... 

Brooks R, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) Charmm A program for macromolecular energy minimization and dynamics calculations. J Comput Chem 4 187-217. 

The early version of the molecular dynamics program CHARMM (22) also... 

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