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

Hannes Loeffler Hannes.Loeffler at stfc.ac.uk
Tue Sep 13 08:05:06 CEST 2016

Hi Stefano,

you might be better off either inspecting the code yourself or
contacting the developers directly (the Gromacs developer list may be
open to this).


On Mon, 12 Sep 2016 18:52:42 +0000
BOSISIO Stefano <s1374284 at sms.ed.ac.uk> wrote:

> 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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