next     upMain HomePage
Next: INTRODUCTION
 

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 tex2html_wrap_inline629 O and H tex2html_wrap_inline629tex2html_wrap_inline633 ) and to polipeptides.

    The results obtained for H tex2html_wrap_inline629 O and H tex2html_wrap_inline629tex2html_wrap_inline633 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 tex2html_wrap_inline641 helix structure, probably because the number of hydrogen bonds are insufficient to maintain the helical array. On the contrary, the icoalanin molecule forms an tex2html_wrap_inline641 helix structure. We obtain this structure simulating all tex2html_wrap_inline645tex2html_wrap_inline647 pairs using only few steps as compared to conventional methods.

Keywords: Simulated Annealing, Molecular Dynamics, Tsallis machine.


 
 

M. A. Moret
-Departamento de Ciências Exatas - UEFS
44100 - Feira de Santana (Ba) - BRASIL
moret@tupan.biof.ufrj.br

P. G. Pascutti
Instituto de Física Carlos Chagas Filho- USP
Rio de Janeiro (RJ) - BRASIL
pascutti@biof.ufrj.br

P. M. Bisch
Instituto de Biofísica Carlos Chagas Filho- UFRJ,
Rio de Janeiro (RJ) - BRASIL,
pmbisch@biof.ufrj.br 

K.C. Mundim
-Instituto de Química, UnB, Caixa Postal 4478,

Brasília, DF, 70904-970, Brasil
kcmundim@unb.br