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How do I set up Jumping Between Wells (JBW) or Free Energy Perturbation (FEP) computations with MacroModel?

April 26, 2017computations energy FEP Free jbw jumping macromodel perturbation Wells

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How do I set up Jumping Between Wells (JBW) or Free Energy Perturbation (FEP) computations with MacroModel?

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There is no mechanism in the Maestro interface to set up these advanced procedures. To perform these simulations, it is necessary to manually create the MacroModel command files. See the MacroModel Reference Manual for sample MacroModel command files and discussion.