Can I obtain minimized structures from MacroModel dynamics simulations?

Yes. During dynamics simulations, you can sample structures at regular intervals. These structures are not minimized, but there is a feature to perform a post-dynamics minimization on all sampled structures. In Maestro, choose Applications → MacroModel → Dynamics, and in the Monitor tab, select the option "Minimize sampled structures". The minimization criteria in the Mini tab will be applied to each sampled structure. If a substructure was used, it will be applied in the minimization also.

Keywords: Maestro, MacroModel, minimize

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