From: Yaxin An (yxan2016_at_gmail.com)
Date: Fri Dec 08 2017 - 08:57:01 CST
Thanks for the kind reply.
I actually saw larger fluctuation of sampling at the interface. Here, I
should use one window across the complete interface? That is to say, if
the interface was at 20A, I should use 15-25 A in this window, right?
When you say ABF is not the method of choice to compute free energies of
hydration, you mean other methods like TI are better choices? In some
papers, TI was used to calculate the free energy of hydration.
Thanks very much.
On Fri, Dec 8, 2017 at 7:39 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> 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
> 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--001a114a8022a876a1055fd56565--
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