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Symplectic quaternion scheme for biophysical molecular dynamics

Miller, T. F., III and Eleftheriou, M. and Pattnaik, P. and Ndirango, A. and Newns, D. and Martyna, G. J. (2002) Symplectic quaternion scheme for biophysical molecular dynamics. Journal of Chemical Physics, 116 (20). pp. 8649-8659. ISSN 0021-9606. doi:10.1063/1.1473654.

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Massively parallel biophysical molecular dynamics simulations, coupled with efficient methods, promise to open biologically significant time scales for study. In order to promote efficient fine-grained parallel algorithms with low communication overhead, the fast degrees of freedom in these complex systems can be divided into sets of rigid bodies. Here, a novel Hamiltonian form of a minimal, nonsingular representation of rigid body rotations, the unit quaternion, is derived, and a corresponding reversible, symplectic integrator is presented. The novel technique performs very well on both model and biophysical problems in accord with a formal theoretical analysis given within, which gives an explicit condition for an integrator to possess a conserved quantity, an explicit expression for the conserved quantity of a symplectic integrator, the latter following and in accord with Calvo and Sanz-Sarna, Numerical Hamiltonian Problems (1994), and extension of the explicit expression to general systems with a flat phase space.

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Miller, T. F., III0000-0002-1882-5380
Additional Information:© 2002 American Institute of Physics. Received 11 January 2002; accepted 5 March 2002. This work was supported by grants PRF-32139-AC, NSF-CHE-9625015, NSF-EIA-0081307 (G.J.M.), and IBM (all authors). The authors would like to thank Professor B.B. Laird and Professor R. Skeel for helpful comments.
Subject Keywords:molecular biophysics, molecular dynamics method, digital simulation, biology computing, parallel processing
Issue or Number:20
Record Number:CaltechAUTHORS:MILjcp02b
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:11061
Deposited By: Archive Administrator
Deposited On:25 Jun 2008
Last Modified:08 Nov 2021 21:13

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