Next: Molecular Dynamics (MD) Simulation
Up: Classical Simulation and Modeling
Previous: Questions We Can Ask
Function optimization is a calculation that pervades much of numerical analysis.
In the context of macromolecules, the function to be optimized (minimized) is an energy. The energy landscape of a biomolecule
possesses an enormous number of minima, or conformational substates. Nonetheless, the goal of energy minimization is simply to find
the local energy minimum, i.e., the bottom of the energy well occupied by the initial conformation ( in figure).
The energy at this local minimum may be much higher than the energy of the global minimum. Physically, energy minimization corresponds
to an instantaneous freezing of the system; a static structure in which no atom feels a net force corresponds to a temperature of 0 K.
In the early 1980's, energy minimization was about all one could afford to do and was dubbed `molecular mechanics.'
|Energy minimization seeks the energy minimum nearest the starting (marked by star) conformation.