Local elevation: A method for improving the searching properties of molecular dynamics simulation
Abstract
The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.
- Publication:
-
Journal of Computer-Aided Molecular Design
- Pub Date:
- December 1994
- DOI:
- 10.1007/BF00124016
- Bibcode:
- 1994JCAMD...8..695H
- Keywords:
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- Conformational search;
- Computer simulation;
- Molecular dynamics;
- Cyclosporin A