Local elevation: a method for improving the searching properties of molecular dynamics simulation.
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.
Huber
T
T
Physical Chemistry, ETH Zentrum, CH-8092 Zürich, Switzerland.
Torda
A E
AE
van Gunsteren
W F
WF
D000465:Algorithms; D003198:Computer Simulation; D017076:Computer-Aided Design; D016572:Cyclosporine / Q000737:chemistry; D015195:Drug Design; D008956:Models, Chemical; D008968:Molecular Conformation; D010420:Pentanes / Q000737:chemistry; D012985:Software Design; D013816:Thermodynamics
D010420:Pentanes; C033353:pentane; D016572:Cyclosporine