Schrodinger, LLC

Yuqing Deng

Byungchan Kim

Robert L Abel

Lingle Wang

Yujie Wu

A method for computing free energy difference between a reference molecule and a target molecule. The target molecule has the common set of atoms Pand a set of atoms P. The method includes applying a potential to restrain an interaction of the additional atomic component from the set of atoms Pwith the common set of atoms Pin the initial state. The method includes determining one or more transition states along a transformation path between the initial state and target state. The method includes scaling the restrain potential correspondingly along the transformation path until the potential becomes zero when a corresponding end state is reached, and calculating the free energy difference between the reference molecule and the target molecule using a value obtained along the transformation path from the initial state to the target state.

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Yuqing Deng