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Stochastic Molecular Optimization Using
Generalized Simulated Annealing
M. A. Moret - P. G. Pascutti - P. M. Bisch and K. C. Mundim
We propose a stochastic optimization
technique based on GSA - Generalized Simulated Annealing 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. Further, unlike usual Molecular Dynamics (MD) method,
the method proposed in this paper is force independent, i.e., we obtain
the optimized conformation without calculating the force, only potential
energy is involved. Therefore, we don't 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 (H 
O and H
O 
) and to polipeptides.
The results obtained for H
O and H
O
using Tsallis thermostatistics suggest that the GSA approach is faster
than the other two conventional machines (Boltzmann and Cauchy machines).
The results for polipeptides show that pentalanin does not form stable 
helix structure, probably because the number of hydrogen bonds are insufficient
to maintain the helical array. On the contrary, the icoalanin molecule
forms an
helix structure. We obtain this structure simulating all 
, 
pairs using only few steps as compared to conventional methods.
Keywords: Simulated Annealing,
Molecular Dynamics, Tsallis machine.
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M. A. Moret
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P. G. Pascutti
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P. M. Bisch
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K.C. Mundim
Brasília, DF, 70904-970, Brasil
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