An algorithm to filter out packing arrangements based on steric clashes
Language English Country Germany Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
- MeSH
- Algorithms * MeSH
- Crystallography MeSH
- Molecular Conformation MeSH
- Models, Molecular MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
This document outlines the use of an algorithm to filter out impossible crystal-packing arrangements based on steric considerations. Within an exhaustive grid search frame, the space sample is reduced by analysis of spherical areas where atom pairs from different rigid units might clash. This technique finds areas in the state space where the global energy minimum might lie. The minimum can then be found by the usual methods of molecular modeling restricted to these particular areas. Only a tiny fraction of atom pair distances need to be tested; usually a single quantity on average per one state of model space! For example, a crystal of three rigid molecules, each containing 12 atoms, has 3x12x12=432 atom pairs just in one unit cell but our method needs to test on average 1 to 4 atom pairs per state. Using modern computers, about 10(12-15) models can be tested within several hours or days. For example, a crystal model with six rotational degrees of freedom (two rigid molecules in the unit cell) each with step 3 degrees can be tested in a few hours on a 1-GHz x86 processor-based machine. The method presented here has been implemented in the SUPRAMOL program.
