[gmx-developers] The role of Jacobian factor in alchemical free energy simualtion

[BOSISIO Stefano]

Dear Gromacs staff,

I am trying to understand some internal issues between my code and Gromacs in alchemical free energy calculations.

Considering a simple alchemical free energy calculation (e.g ethane to methanol) with a constraint applied to all the hydrogen bonds  does Gromacs calculate a Jacobian correction ? (Boresch Stefan, and Martin Karplus "The Jacobian factor in free energy simulations." The Journal of chemical physics105.12 (1996): 5145-5154  )
Alternatively, does Gromacs apply any correction to the computed free energy changes if constraints were applied to a solute?


Thank you

Best regards,

Stefano

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