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Chapter 2

Newton Euler Inverse Mass Operator (NEIMO) Dynamics of Polypeptides

Abstract:

Newton-Euler Inverse Mass Operator (NEIMO) Dynamics is a fast method for calculating internal-coordinate molecular dynamics. Unlike other exact methods for solving these equations of motion, computational time for the NEIMO method is proportional to , rather than , where is the number of degrees of freedom. This allows internal-coordinate dynamics to be solved for very large systems. The first use of the NEIMO method for molecular dynamics is presented here. Results are given for simulations of a wide range of peptide and protein systems. The computational time is shown to be rigorously proportional to . Additionally, the dynamics are shown to be accurate for timesteps much larger than those used in Cartesian-coordinate dynamics. For small peptides, timesteps as large as 20 fs are achievable.



ktl@sgi1.wag.caltech.edu
Sat Jun 18 14:06:11 PDT 1994