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Can a Simulated Annealing procedure be performed with MacroModel?

Yes, you can do simulated annealing dynamics with MacroModel. It is necessary to start such simulations from the command line; these jobs are not available from Maestro. There is a simulated annealing example in the Dynamics chapter of the MacroModel User Manual. In addition, there are alternative examples (one stepwise, one continuous) in the MacroModel test directory at


The MacroModel instruction file, with most of the dynamics information, can be generated from Maestro. You must then modify the .com file to add the details of temperature, etc, as in the examples. If you are using the substructure mechanism, Maestro can also help to generate the .sbc file.

A stepwise heating procedure can also be accomplished by reversing the heating progression relative to simulated annealing.

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