[gmx-users] The role of Jacobian factor in free energy simulations

BOSISIO Stefano s1374284 at sms.ed.ac.uk
Mon Sep 12 20:52:47 CEST 2016

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,


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