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] Free energy change and volume of the box

[Hannes Loeffler]

Have you had a look at
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme

to see if that technique would be applicable to you and look through
the references given?  When you do absolute transformations you will
need to think about standard state (and standard volume).


On Thu, 13 Oct 2016 15:33:47 +0200
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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