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

BOSISIO Stefano s1374284 at sms.ed.ac.uk
Tue Sep 13 17:24:13 CEST 2016


Thanks for the answer.

Thus, taking a constrained bond length, which is alchemically transformed, the only term that comes into play is the mass metric tensor, isn't it?
Is there any piece of code of Gromacs which is designated to correct this issue, you could address me?

Best wishes,


From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> on behalf of Berk Hess <hess at kth.se>
Sent: 13 September 2016 12:02
To: gmx-developers at gromacs.org
Subject: Re: [gmx-developers] The role of Jacobian factor in alchemical free energy simualtion


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 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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