Python Programming for Biology: Bioinformatics and Beyond

Figure 25.4 (Plate 11).  An overview of the simulated annealing procedure, as

applied to a molecular structure. The method of simulated annealing can be applied to

the problem of computing a molecular structure given information relating to the bonding

and non-bonding forces between atoms. Starting from random positions the forces that

result from a particular arrangement of atoms can be estimated using knowledge of the

forces’ energy potentials. In turn this leads to a dynamics simulation where the forces,

momenta and thus changes of atomic position can be modelled at discrete time steps. By

applying an annealing schedule with a decreasing effective temperature, the simulated

kinetic energy of the atoms will initially be large, so that large differences in conformation

can be explored, but end up making only small adjustments, to better home in on a precise

solution.