Unification of box shapes in molecular simulations

✍ Scribed by Bekker, H.

• Book ID: 101220683
• Publisher: John Wiley and Sons
• Year: 1997
• Tongue: English
• Weight: 317 KB
• Volume: 18
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/(sici)1096-987x(19971130)18:15<1930::aid-jcc8>3.0.co;2-p

✦ Synopsis

In molecular simulations with periodic boundary conditions the computational box may have five different shapes: triclinic; the hexagonal prism; two types of dodecahedrons; and the truncated octahedron. In this article, we show that every molecular simulation, formulated in one of these boxes, can be transformed into a simulation in one of the other ones. The transformation can be done in a preprocessing phase. The simulation in the new box is exactly identical to the simulation in the original one. This means that every molecular simulation may be done in the same type of box. Because the triclinic box is the easiest one to implement, we pay special attention to how to transform the other four box types into triclinic boxes. As a consequence, simulations in the often used truncated octahedron are superfluous; they may be done in a much simpler way in a triclinic box.