References   STOCHASTIC MOLECULAR OPTIMIZATION USING APPLICATIONS

 

CONCLUDING REMARKS

We conclude with this preliminary study that the SMO approach is an excellent qualitative and quantitative indicator of conformational molecular preferences.

-The GSA method, compared with he gradient descent approach, or other conventional approach, shows the advantage to obtain directly the global minimum, while scanning the potential hyper surface during this searching.

-Further, unlike usual Molecular Dynamics (MD) method, the SMO 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.

-We emphasize that using MD method, with a reasonable computer time, it is not guaranteed that a global minimum structure will be crossed or reached during the simulation. However the SMO method guarantees that a global minimum will be attained, at least, as shown in this paper for peptides of order of 20 residues. Further this procedure enables us to map out minima while searching for the global minimum.

-The GSA method converges quickly when the q parameter falls within (14).

- We obtained the same behavior as in [14] by using an inverse visiting distribution probability, calculated by (11).

We hope to apply the SMO method to simulate a peptide at the membrane interfaces and to investigate other molecular structures, such as pharmacs, proteins and DNA, which are more complex in structure than those used in this paper.\