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Random Simulated Annealing
The example input file below shows how to produce a family of coordinates using simulated annealing starting from random coordinates (Nilges, Clore, and Gronenborn, 1988b). The example file is general and should work for all types of macromolecules, although it has been tested only for proteins of up to 2400 atoms. The user might want to change the simulated annealing starting temperature if convergence is unsatisfactory. The duration of the high-temperature stage is internally determined. The filenames of the family of coordinates obtained by this protocol are “random 1.pdb" through “random 10.pdb". These coordinates usually require extensive regularization by using the “dgsa.inp" protocol (Section 38.3.3). Note that the “dgsa.inp" protocol requires the template coordinates even though the “random.inp" does not.
Xplor-NIH 2024-09-13