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%.
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Bekker, H., van den Berg, J.P., Wassenaar, T.A. (2003). Constructing a Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with Periodic Boundary Conditions. In: Sloot, P.M.A., Abramson, D., Bogdanov, A.V., Gorbachev, Y.E., Dongarra, J.J., Zomaya, A.Y. (eds) Computational Science — ICCS 2003. ICCS 2003. Lecture Notes in Computer Science, vol 2659. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44863-2_8
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DOI: https://doi.org/10.1007/3-540-44863-2_8
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