A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints
✍ Scribed by Henk Bekker; Jur P. Van Den Berg; Tsjerk A. Wassenaar
- Publisher
- John Wiley and Sons
- Year
- 2004
- Tongue
- English
- Weight
- 223 KB
- Volume
- 25
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
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. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1037–1046, 2004