[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 <alexanderwien2k at gmail.com<mailto:alexanderwien2k at gmail.com>> 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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