Substructured molecular dynamics using multibody dynamics algorithms

R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson, Intl J of Non-Linear Mechanics, 43, 1045-1055 (2008).

This paper reports a new research effort aimed at using efficient multibody dynamics methods to simulate coarse-grained molecular systems. Various molecular systems are studied and the results of nanosecond-long simulations are analyzed to validate the method. The systems studied include bulk water, alkane chains, alanine dipeptide and carboxyl terminal fragments of calmodulin, ribosomal L7/L12 and rhodopsin proteins. The stability and validity of the simulations are studied through conservation of energy, thermodynamics properties and conformational analysis. In these simulations, a speed up of an order of magnitude is realized for conservative error bounds with a fixed timestep integration scheme. A discussion is presented on the open-source software developed to facilitate future research using multibody dynamics with molecular dynamics.

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