

Preprint 136/2006
Objective molecular dynamics
Traian Dumitrică and Richard D. James
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Submission date: 20. Nov. 2006
Pages: 32
published in: Journal of the mechanics and physics of solids, 55 (2007) 10, p. 2206-2236
DOI number (of the published article): 10.1016/j.jmps.2007.03.001
Bibtex
Keywords and phrases: Atomistic structures, numerical algorithms
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Abstract:
We introduce a generalization of periodic molecular dynamics that we term objective
molecular dynamics. It is a method of doing classical molecular dynamics for a restricted set of
atoms, nonperiodically mapping the time-dependent displacements of this small set of atoms onto
the full, typically infinite structure, such that the full structure satisfies exactly the full, unconstrained
set of equations of molecular dynamics subject to certain group-invariant initial conditions.
The method is applicable to a wide variety of interesting molecular structures including the tails,
capsids and other parts of many viruses, carbon nanotubes, many of the common proteins, C60 and
many other nanostructures now being synthesized, especially via the process of self-assembly. The
method is illustrated by simulations of carbon nanotubes.