A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints
Copyright 2004 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 25(2004), 8 vom: 27. Juni, Seite 1037-46 |
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| Weitere Verfasser: | , |
| Format: | Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2004
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Proteins |
| Zusammenfassung: | Copyright 2004 Wiley Periodicals, Inc. 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 |
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| Beschreibung: | Date Completed 09.06.2004 Date Revised 06.04.2004 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |