[gmx-users] The role of Jacobian factor in free energy simulations
s1374284 at sms.ed.ac.uk
Tue Sep 13 09:50:40 CEST 2016
Thanks Hannes for the suggestion
I will write on the other mailing list
> 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).
> 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,
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
More information about the gromacs.org_gmx-users