title: A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints.
abstract: 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.
authors.affiliation: Institute for Mathematics and Computing Science, University of Groningen, P.O.B. 800 9700 AV Groningen, The Netherlands. bekker@cs.rug.nl
authors.forename: Henk
authors.initials: H
authors.lastname: Bekker
authors.forename: Jur P
authors.initials: JP
authors.lastname: van den Berg
authors.forename: Tsjerk A
authors.initials: TA
authors.lastname: Wassenaar
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins