[gmx-users] binding free energy

[André Farias de Moura]

Hi Alex,

if you use an alchemical method, your answer will be a complex mixture of
solvation and adsorption free energy, since the molecule may diffuse
freely, so it might be closer or farther from the surface depending on your
initial setup, simulation parameters, length of the simulation and so on.

It can be done, but I'd say the physics would always be blurred even if the
simulations were well converged. For instance, a larger box with more water
would have a larger bulk character if the surface area of the solid is kept
constant.

IMHO, you have to split the problem in two well-defined models: standard
alchemical methods should be used without the surface (providing the
solvation free energy) and a pmf calculation should be done to evaluate the
free energy profile to bring the molecule from the bulk solution to the
interface. The latter can be done by means of equilibrium distributions or
using non-equilibrium methods (umbrella sampling and steered MD).

I hope it helps.

Andre

On Mon, Jul 4, 2016 at 11:14 AM, Alexander Alexander <
alexanderwien2k at gmail.com> wrote:

> Dear gromacs user,
>
> I was wondering if anybody has any experience with binding free energy
> calculation of a molecule (here amino acid) into a solid surface in aqueous
> solution using alchemical analysis?
>
> I have already tried successfully the tutorial of methane solvation free
> energy in water and some other examples, but looks all of them are
> solvation free energy and not binding free energy!
>
> Thanks.
> Regards,
> Alex
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090