From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Jul 18 2020 - 07:36:17 CDT
With CG you get better statistical convergence, but with atomistic it'd be
definitely more accurate at describing the intermolecular potential. So do
your trials with CG, and see there if you can get a decently converged PMF.
As for the method of choice, it depends on which variable you use. For
simpler ones like distances, you can use everything including straight ABF
(relying on the TI gradients). Otherwise, you can use umbrella sampling
(traditional or exchange-based), eABF, metadynamics, etc.
The BFE tutorial is useful, but a lot of it covers the degrees of freedom
involved with the rotations of the two objects. The effect of the solvent
is not discussed there much, because water relaxes quickly. A lipid
membrane is several orders of magnitude slower.
It's unclear from the email how familiar are you with FE computations, but
I would start from the simple and cheapest examples. Some of them are
where there are pre-made NAMD inputs for two tiny systems using a variety
of methods. The full documentation is here:
or in one of the chapters of the NAMD user's guide.
For more complex tasks that involve multiple steps, some of the tutorials
may be useful. Do keep in mind, however, that most of them are not kept up
to date. There are generally new literature papers published every year
with useful new ideas. Check those, too.
In summary, this computation is wholly not trivial but is becoming
increasingly feasible over the years.
On Fri, Jul 17, 2020 at 9:08 PM Ethan Croitoru <ecroitoru1_at_gmail.com> wrote:
> I am trying to calculate the free-energy of association of two
> transmembrane helices, and am looking for tips. For instance if I should
> use a coarse-grained model or all atom simulation, an implicit or
> explicit membrane, and use umbrella sampling or the extended ABF from the
> binding free-energy tutorial.
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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