Molecular mechanics steepest descent

Algorithm used for the minimization of mathematical functions (steepest descent, gradient, second-derivative and other methods). In molecular mechanics these are used to minimize the strain energy and thereby optimize the molecular structure (see molecular mechanics). 

Select the Molecular mechanics menu and choose Steepest descent as the initial Minimizer that can be changed to Conjugated gradient later. 

A reaction-path based method is described to obtain information from ab initio quantum chemistry calculations about the dynamics of energy disposal in exothermic unimolecular reactions important in the initiation of detonation in energetic materials. Such detailed information at the microscopic level may be used directly or as input for molecular dynamics simulations to gain insight relevant for the macroscopic processes. The semiclassical method, whieh uses potential energy surface information in the broad vicinity of the steepest descent reaction path, treats a reaction coordinate classically and the vibrational motions perpendicular to the reaction path quantum mechanically. Solution of the time-dependent Schroedinger equation leads to detailed predictions about the energy disposal in exothermic chemical reactions. The method is described and applied to the unimolecular decomposition of methylene nitramine. 

A molecular mechanics optimization allo vs partial to full atom flexibility of the protein through an energy minimization of the protein-ligand complexes and can be used for postprocessing of docked poses. In favor of that, various minimization methods ranging from a steepest descent to a genetic algorithm can be used [67]. 

HyperChem s optimizers (steepest descent, Fletcher-Reeves, and Polak-Ribiere conjugate-gradient methods, and the block diagonal Newton-Raphson) differ in their generality, convergence properties, and computational requirements. They are unconstrained optimization methods however, it is possible to restrain molecular mechanics and quantum mechanics calculations in HyperChem by adding extra restraining forces. 

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