From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Dec 08 2017 - 06:39:06 CST
Hi,
First, ABF is not the method of choice to compute free energies of
hydration, unless you are interested in the hydration mechanism when the
solute crosses the interface. But it should work anyway.
Second, fluctuations of the shape and structure of the interface are going
to be the main obstacle to convergence here. Actually splitting into
several windows may do more harm than good here, because it may trap the
system in local minima. I would use a single window spanning the complete
interface.
Best,
Jerome
On 8 December 2017 at 00:22, Yaxin An <yxan2016_at_gmail.com> wrote:
> Hi All:
>
> I am running ABF simulations for the free energy of hydration of alkanes.
> But I got different values for the free energies every time when I repeat
> the simulations, like 1.5 and 3.0 Kcal/mol.
>
> In the simulation, there was one water box (40 Angstrom by40 by 40). The
> reaction coordinate is the Z distance between COM of the water box and the
> one alkane molecule. The reaction coordinate spans from 0 to 45.
>
> I split the reaction coordinate into 9 windows: 0-5, 5-10, ....,40-45. And
> I ran the simulation in each window for 50 ns. Each time the free energy
> converged. But when I repeated it, the free energy converged to a different
> value.
>
> Hope someone can give me some suggestion.
>
> Thanks
> Yaxin
>
>
>
>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:44 CST