J Chem Theory Comput. 2008 Mar;4(3):468-76. doi: 10.1021/ct700192z.

Molecular Graphics of Convex Body Fluids.

Journal of chemical theory and computation

Adrian T Gabriel, Timm Meyer, Guido Germano

PMID: 26620787 DOI: 10.1021/ct700192z

Abstract

Coarse-grained modeling of molecular fluids is often based on nonspherical convex rigid bodies like ellipsoids or spherocylinders representing rodlike or platelike molecules or groups of atoms, with site-site interaction potentials depending both on the distance among the particles and the relative orientation. In this category of potentials, the Gay-Berne family has been studied most extensively. However, conventional molecular graphics programs are not designed to visualize such objects. Usually the basic units are atoms displayed as spheres or as vertices in a graph. Atomic aggregates can be highlighted through an increasing amount of stylized representations, e.g., Richardson ribbon diagrams for the secondary structure of proteins, Connolly molecular surfaces, density maps, etc., but ellipsoids and spherocylinders are generally missing, especially as elementary simulation units. We fill this gap providing and discussing a customized OpenGL-based program for the interactive, rendered representation of large ensembles of convex bodies, useful especially in liquid crystal research. We pay particular attention to the performance issues for typical system sizes in this field. The code is distributed as open source.

Publication Types

• Journal Article