Coarse-grained modeling of molecular fluids is often based on non-spherical 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 a protein, 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 feld. The code is distributed as open source.
|The mixture and spherocylinder systems were kindly provided by David Cheung and Paul O'Brien, Molecular Simulation Group (Prof. Michael P. Allen), Department of Physics, University of Warwick, UK.|
Program download and online manual. Reference (please cite when using QMGA for a scientific publication):
Adrian T. Gabriel, Timm Meyer, Guido Germano, "Molecular graphics of convex body fluids", J. Chem. Theory Comput. 4, 468-476 (2008), DOI 10.1021/ct700192z, free download by courtesy of ACS, corrections.
See also the conference poster (29 MB) shown at the Rhein-Main Modelling Meeting in Mainz on 15 June 2007, at the Materialforschungstag Mittelhessen in Rauischolzhausen on 6 July 2007, at the CCP2007 - Conference on Computational Physics in Brussels on 5-8 September 2007, and at the NIC-Symposium 2008 in Jülich on 20-22 February 2008.
Send feedback and questions to qmgausers.sourceforge.net.
Main developer: Adrian Gabriel, Computer Simulation Group (Prof. Guido Germano), Department of Chemistry, Philipps-University Marburg, Germany.
Please send donations by bank transfer to Philipps-Universität Marburg, account number 108, Sparkasse Marburg-Biedenkopf, BLZ 533 500 00, IBAN DE 30 5335 0000 0000 0001 08, BIC HELADEF1MAR, with the motivation "Spende zu Gunsten des Kontos 81503494" (without this number in the motivation the money cannot be identified as being meant for the Computer Simulation Group and will be lost within the central administration's budget). Alternatively, you may use the button below and benefit the PayPal account of the main developer, with 5% going to SourceForge.