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Calculating near-densest lattice packings of non-convex objects to minimize computational box volumes in Molecular Dynamics simulations

Berg, J. van den (2003) Calculating near-densest lattice packings of non-convex objects to minimize computational box volumes in Molecular Dynamics simulations. Master's Thesis / Essay, Computing Science.

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Abstract

In chemistry, much CPU time is spent nowadays on Molecular Dynamics simulations to gain insight in the functioning of biophysical processes. In many of these simulations, the simulated system consists of a computational box with a single macro-molecule 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 this may be done by constructing a computational box with minimal volume. It has been shown that the problem of finding minimal computational boxes can be reformulated as the mathematical problem of finding densest lattice packings of non-convex objects. In this paper, a method is presented to approximate such densest lattice packings. We use this method to calculate near-minimal computational boxes for a significant number of macro-molecules. These boxes prove to have typically 50% less volume than conventional boxes, and as a result the simulation time also decreases with typically 50%. For oblong molecules, this ratio can even be 80%.

Item Type: Thesis (Master's Thesis / Essay)
Degree programme: Computing Science
Thesis type: Master's Thesis / Essay
Language: English
Date Deposited: 15 Feb 2018 07:30
Last Modified: 15 Feb 2018 07:30
URI: http://fse.studenttheses.ub.rug.nl/id/eprint/8886

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