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