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.
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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