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

[BOSISIO Stefano]

Thanks Hannes for the suggestion
I will write on the other mailing list

Best regards,
Stefano



> On 13 Sep 2016, at 07:06, Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk> wrote:
> 
> 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).
> 
> Cheers,
> Hannes.
> 
> 
> 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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