The following two example input files demonstrate how to use simulated annealing (Kirkpatrick, Gelatt, and Vecchi 1983) through molecular dynamics in crystallographic refinement (SA-refinement). The ``check.inp" protocol should be carried out before running this protocol.
The first step is the preparation stage of SA-refinement . It consists of several cycles of minimization in order to relieve strain or bad contacts of the initial coordinates. The repel nonbonded energy function (Eq. 4.8) should be tried if the minimization does not converge or exits with ``line search abandoned" and van der Waals energies in the thousands of kcal mole (cf. 13.1.1).
Now we are ready for simulated annealing. The following example represents the so-called slow-cooling protocol (Brünger, Krukowski, and Erickson 1990). When higher initial temperatures are used, one has to decrease the time step; e.g., one should use a 0.5 fsec time step at 4000K.
If the temperature gets too high and the system blows up, one should try to reduce the time step or decrease the temperature. The final coordinates (``slowcool.pdb") are already minimized, unlike earlier protocols, which required a final stage.