About this document STOCHASTIC MOLECULAR OPTIMIZATION USING CONCLUDING REMARKS

References

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Tsallis, C., and Stariolo, D. A., Phys. A 233, 395 (1996).

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Arêas, E. P. G., Pascutti, P. G., Schreier, S., Mundim, K. C., Bisch, P. M., J. Phys. Chem., 99, 14882 (1995).

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Arêas, E. P. G., Pascutti, P. G., Schreier, S., Mundim, K. C., Bisch, P. M., Brazilian J. Med. Biol. Res., 27, 527 (1994).

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The GSA_ND routine was build up by Moret, M. A., S. G., and Mundim, K. C. (1995).

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Mundim, K. C., Tsallis, C., Int. J. Quant. Chem., 58 (4), 373 (1996).

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Ceperly, D., Alder, B., Science, 231, 555 (1986).

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Tsallis, C., J. Stat. Phys., 52, 479 (1988).

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Curado, E. M. F., and Tsallis, C., J. Phys A, 24, L69 (1991); Corrigenda: J.Phys. A, 24, 3187 (1991) and, 25, 1019 (1992).

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Moret, M. A., S. G., Lameirre, T. and Mundim, K. C., ''An Improved Version of the GSA'', Internal note (1996).

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Berendsen, H. J. C., ''Molecular Dynamics Simulations of Statistical Mechanical System'', Part III, North-Holland Amsterdan, (1986).

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Tsallis, C., Souza, A. M., and Maynard, R., ''Lévy-Flight and Related Topics in Physics'', Spring-Verlag, Heidelberg (1995).

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Tables

TABLE- I.a. In this table all bond stretching parameters are listed. is in kcal mol and is in

TABLE- I.a. In this table all bond stretching parameters are listed. is in kcal mol and is in

TABLE-I.c. This table shows all improper dihedral angle parameters. is in kcal mol rad and is in degrees.

TABLE-I.d. This table shows all improper dihedral angle parameters. is in kcal mol and is in degrees.

TABLE-I.e. In this table all used atomic mass in AU are listed.

Captions to Figures

FIGURE 1. This figure shows the used procedure in this paper to make the coupling between the Molecular Mechanics package (THOR) and the Generalized Simulated Annealing (GSA).

FIGURE 2. This figure shows the range of the q parameter. When q is close to 1.7 the algorithm convergence is faster than other q values. This behavior is obtained for the water molecule when we optimize H-O-H angle.

FIGURE 3. This figure shows the range of the q parameter. When q is close to 1.6 the algorithm convergence is faster than other q values. This behavior is obtained for the H O molecule when we optimize H-O-O angle.

FIGURE 4. The figure shows the potential surface by optimizing the two proper dihedral angles for the H O molecule. The angular symmetry is observed in the - surface.

FIGURE 5. The global minimum for the and angles, is close to 300 (-60 ) and 320 (-40 ), respectively. This behavior, for the icoalanin molecule, is an helix structure.

About this document STOCHASTIC MOLECULAR OPTIMIZATION USING CONCLUDING REMARKS