Conformational energy minimization by simulated annealing using molecular dynamics: Some improvements to the monitoring procedure

Abstract

Abstract The possibility of using molecular dynamics techniques as a tool for simulated annealing is tested in the case of the molecule of biological interest N‐acetyl, N′‐methyl amides of 3(S)‐hydroxy, 4(S)‐amino 6‐methyl heptanoic acid [(3S, 4S)‐statine] and of its (3R,4S) diastereomer. The approach is able to reach global minimum in the conformational space in the case of the mentioned molecule. A description of the method is given. The use of fractional fluctuations of the internal potential energy as an indicator able to point out transition from a given minimum region to a deeper one is investigated. The results about the lowest energy conformation of (3S,4S) diastereomer are in fairly good accordance with the results obtained in the case of search within the whole Conformational hyperspace.