From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Dec 08 2017 - 09:27:21 CST
That's possible, but the TI formalism can be applied just as well to a
geometric variable (i.e. a Cartesian coordinate) or the "lambda" switching
parameter in an alchemical. In the latter case, you can also use the FEP
estimator for the free-energy.
The bottom line is that a geometric calculation (ABF, metadynamics,
umbrella sampling) will give you an entire PMF, instead of a free energy
difference (i.e. a single number) that you get in alchemical runs. The
additional information usually means larger sampling times are required.
On Fri, Dec 8, 2017 at 9:57 AM, Yaxin An <yxan2016_at_gmail.com> wrote:
> Hi Jérôme;
> 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:
> > 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
> > 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
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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