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A method to obtain a near‐minimal‐volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints
Author(s) -
Bekker Henk,
Van Den Berg Jur P.,
Wassenaar Tsjerk A.
Publication year - 2004
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20050
Subject(s) - periodic boundary conditions , macromolecule , molecular dynamics , volume (thermodynamics) , radius , boundary (topology) , rotation around a fixed axis , molecule , boundary value problem , lattice (music) , statistical physics , materials science , physics , mathematics , chemistry , thermodynamics , computer science , classical mechanics , mathematical analysis , computational chemistry , biochemistry , computer security , quantum mechanics , acoustics
If the rotational motion of a single macromolecule is constrained during a molecular dynamics simulation with periodic boundary conditions it is possible to perform such simulations in a computational box with a minimal amount of solvent. In this article we describe a method to construct such a box, and test the approach on a number of macromolecules, randomly chosen from the protein databank. The essence of the method is that the molecule is first dilated with a layer of at least half the cut‐off radius. For the enlarged molecule a near‐densest lattice packing is calculated. From this packing the simulation box is derived. On average, the volume of the resulting box proves to be about 50% of the volume of standard boxes. In test simulations this yields on average a factor of about two in simulation speed. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1037–1046, 2004
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