Summary: Substructured Molecular Dynamics using Multibody Dynamics
Rudranarayan M. Mukherjee a,1
aRensselaer Polytechnic Institute, 110 8th Street, Troy NY 12180 U.S.A.
Paul S. Crozier b
bSandia National Laboratories, Albuquerque, New Mexico U.S.A.
Steven J. Plimpton c
cSandia National Laboratories, Albuquerque, New Mexico U.S.A.
Kurt S. Anderson d
dRensselaer Polytechnic Institute, 110 8th Street, Troy NY 12180 U.S.A.
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.
Key words: Coarse grained molecular dynamics, Multibody dynamics algorithms, Open source software