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Back to previous unit The effect of solvent and hydrophobic interactions

Potential energy functions

Simulation methods

Energy minimization

Molecular Dynamics

Other methods

S.J. Weiner, P.A. Kollman, D.A. Case, U.C. Singh, G. Alagona, S. Profeta Jr. and Paul. Weiner. "A new force field for the molecular mechanical simulation of nucleic acids and proteins". J. Am. Chem. Soc. , 106:765-784 (1984).

The original paper describing the AMBER potential energy function. An interesting if slightly heavy going paper describing the process of developing an energy function, source of parameters etc.. For further details of the AMBER program and energy function then why not look at the AMBER home page at the University of Calfornia, San Francisco.

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