SubstructuredMolecular Dynamics usingMultibodyDynamics Algorithms

This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include bulk water, alkane chains, alanine dipeptide and carboxyl terminal fragments of calmodulin, ribosomal protein, and rhodopsin. The atomistic representations of these systems include several thousand degrees of freedom and the results of nano-second long simulations of several of these systems are presented. 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 time step integration scheme. A discussion is presented on the open-source software developed to facilitate future research using multibody dynamics with molecular dynamics.