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

[BOSISIO Stefano]

Thanks for the answer.

I am still wondering 2 questions:

1) Calculating the Fixman potential could lead to a correction of this issue?

2) Is Gromacs programmed to correct this issue?

Thank you very much


Best,


Stefano

________________________________
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 16:54:39
To: Discussion list for GROMACS development
Subject: Re: [gmx-developers] The role of Jacobian factor in alchemical free energy simualtion


No, all other interactions that work on the bond length also contribute, i.e. forces from potentials and other connected constraints.

Cheers,

Berk

On Sep 13, 2016 5:24 PM, BOSISIO Stefano <s1374284 at sms.ed.ac.uk> wrote:
Hi,


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,

Stefano

________________________________
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

Hi,

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.

Cheers,

Berk

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,

Stefano




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