Constructing a near-minimal-volume computational box for molecular dynamics simulations with periodic boundary conditions

Authors:
Henk Bekker;Jur P. van den Berg;Tsjerk A. Wassenaar
Affiliations:
Institute for Mathematics and Computing Science, University of Groningen, Groningen, The Netherlands;Institute for Mathematics and Computing Science, University of Groningen, Groningen, The Netherlands;Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biophysical Chemistry, University of Groningen, Groningen, The Netherlands
Venue:
ICCS'03 Proceedings of the 2003 international conference on Computational science: PartIII
Year:
2003

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Abstract

In many M.D. simulations the simulated system consists of a single macromolecule in a solvent. Usually, one is not interested in the behaviour of the solvent, so, the CPU time may be minimized by minimizing the amount of solvent. For a given molecule and cut-off radius this may be done by constructing a computational box with near minimal volume. In this article a method is presented to construct such a box, and the method is tested on a significant number of macromolecules. The volume of the resulting boxes proves to be typically 40% of the volume of usual boxes, and as a result the simulation time decreases with typically 60%.