Stochastic molecular optimization using generalized simulated annealing

Moret MA, Pascutti PG, Bisch PM, Mundim KC

JOURNAL OF COMPUTATIONAL CHEMISTRY
19: (6) 647-657 APR 30 1998

Cited References: 19            Times Cited:  7

Abstract:
        We propose a stochastic optimization technique based on a generalized simulated annealing (GSA) method for mapping minima points of molecular conformational energy surfaces. The energy maps are obtained by coupling a classical molecular force field (THOR package) with a GSA procedure. Unlike the usual molecular dynamics (MD) method, the method proposed in this study is force independent; that is, we obtain the optimized conformation without calculating the force, and only potential energy is involved. Therefore, we do not need to know the conformational energy gradient to arrive at equilibrium conformations. Its utility in molecular mechanics is illustrated by applying it to examples of simple molecules (H2O and H2O3) and to polypeptides. The results obtained for H2O and H2O3 using Tsallis thermostatistics suggest that the GSA approach is faster than the other two conventional methods (Boltzmann and Cauchy machines). The results for polypeptides show that pentalanine does not form a stable alpha-helix structure, probably because the number of hydrogen bonds is insufficient to maintain the helical array. On the contrary, the icoalanine molecule forms an alpha-helix structure. We obtain this structure simulating all Phi, Psi pairs using only a few steps, as compared with conventional methods. (C) 1998 John Wiley & Sons, Inc.

Author Keywords: simulated annealing, molecular dynamics, Tsallis machine

KeyWords Plus:   TSALLIS STATISTICS

Addresses:
Mundim KC, UFBa, Inst Fis, Rua Caetano Moura 123, BR-40210340 Salvador, BA, Brazil.
UFBa, Inst Fis, BR-40210340 Salvador, BA, Brazil.
UEFS, Dept Ciencias Exactas, Feira De Santana, Brazil.
USP, Inst Fis, BR-09500900 Sao Paulo, Brazil.
UFRJ, Inst Biofis, Rio De Janeiro, Brazil.

Publisher: JOHN WILEY & SONS INC, NEW YORK
IDS Number: ZF767
ISSN: 0192-8651