Re: [gmx-users] Free energy change and volume of the box

[BOSISIO Stefano]

Hi Alex,

The free energy does depend on volume
Thus, you should simulate bound and free state with the same volume.
However, this is not necessary, since the error is pretty small usually (in my 
experience)

Here two references:

H?nenberger, Philippe H., and J. Andrew McCammon. "Effect of artificial 
periodicity in simulations of biomolecules under Ewald boundary conditions: a 
continuum electrostatics study." Biophysical chemistry 78.1 (1999): 69-88.


Reif, Maria M., and Philippe H. H?nenberger. "Computation of 
methodology-independent single-ion solvation properties from molecular 
simulations. III. Correction terms for the solvation free energies, enthalpies, 
entropies, heat capacities, volumes, compressibilities, and expansivities of 
solvated ions." The Journal of chemical physics134.14 (2011): 14410

Where volume effects are studied.

Finally, as Hannes said, for absolute binding free energy you have to consider 
standard state correction to compare with experimental "standard" values

Best regards,

Stefano
On 13 Oct 2016, at 14:36, Alex 
> wrote:

Dear gromacs user,

As you know the binding free energy is the difference between the free
energy change inbounded state and unbounded state.

\Delta (\Delta G)_(binding) = \Delta G_(bounded)  - \Delta G_(unbounded).

Then my question is that if it is necessary to simulate the free energy
change of bonded and unbounded states in the identical volume size?

In another meaning if the free energy change (either bounded or unbounded)
is a volume depended quantity?

I am using FEP method to calculate the binding free energy of amino acid
to  a solid surface.

Best regards,
Alex
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Re: [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.loeff...@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 +
> BOSISIO Stefano <s1374...@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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[gmx-users] The role of Jacobian factor in free energy simulations

[BOSISIO Stefano]

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

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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[gmx-users] Gromacs Jacobian in free energy calculations

[BOSISIO Stefano]

Hi everybody  :)

I was wondering how gromacs performs a free energy calculations. In particular, 
for a relative free energy of hydration calculation, via a thermodynamic cycle 
in single topology is the Jacobian calculated?
How did it calculate the free energy if all the bonds are constrained during 
the calculation?
Thank you very much,


Best wishes,

Stefano
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