Steepest descent calculations, potential energy

As explained above, the QM/MM-FE method requires the calculation of the MEP. The MEP for a potential energy surface is the steepest descent path that connects a first order saddle point (transition state) with two minima (reactant and product). Several methods have been recently adapted by our lab to calculate MEPs in enzymes. These methods include coordinate driving (CD) [13,19], nudged elastic band (NEB) [20-25], a second order parallel path optimizer method [25, 26], a procedure that combines these last two methods in order to improve computational efficiency [27],... 

We shall not discuss all the numerous energy minimisation procedures which have been worked out and described in the literature but choose only the two most important techniques for detailed discussion the steepest descent process and the Newton-Raphson procedure. A combination of these two techniques gives satisfactory results in almost all cases of practical interest. Other procedures are described elsewhere (1, 2). For energy minimisation the use of Cartesian atomic coordinates is more favourable than that of internal coordinates, since for an arbitrary molecule it is much more convenient to derive all independent and dependent internal coordinates (on which the potential energy depends) from an easily obtainable set of independent Cartesian coordinates, than to evaluate the dependent internal coordinates from a set of independent ones. Furthermore for our purposes the use of Cartesian coordinates is also advantageous for the calculation of vibrational frequencies (Section 3.3.). The disadvantage, that the potential energy is related to Cartesian coordinates in a more complex fashion than to internals, is less serious. 

Figure 5. The hinge-bending potential for free and bound lysozyme systems (from Bruccoleri et al. 1986) (a) steepest descents protocol (b) spatially constrained protocol. The circles are the points calculated by the protocols, the line is the least-squares fit parabola. All plots are on the same scale with energies in units of kcal/mole and angles in degrees. Positive angles correspond to closing.

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. 

Steepest descent A computational method of traversing a potential energy surface by taking steps that have the greatest change to speed up iterative calculations. 

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