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

Berk Hess hess at kth.se
Tue Sep 13 13:02:30 CEST 2016


In alchemical reactions it is often desirable to avoid changing bond 
lengths by using a topology with atoms from both states present. In that 
case there is no explicit Jacobian involved. If you do change constraint 
lengths, the metric tensor contribution comes in through the constraint 
forces. If you want this effect or not depends on what quantity you want 
to calculate exactly. You can correct for this analytically afterwards.



On 2016-09-13 11:57, BOSISIO Stefano 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 physics/105.12 (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
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

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