From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jul 27 2018 - 22:49:55 CDT
Hello, all.
Not to curb everyone's enthusiasm, but this particular channel has *three*
constriction regions. The innermost one, which is being discussed, is
composed by four histidines. The second innermost one has four tryptophans
packed together even more tightly. Depending on the viral strain there can
be also a tetrad of valines at the outer opening, aptly called a "valve" by
the crystallographers who resolved it.
At four additional variables for every region, that could really get out of
hand.
Kelly, while it would be very effective to use collective variables-based
simulations to compute a PMF, have you thought about initializing the
ligand in multiple positions and run regular MD simulations on each one?
If done carefully, this could actually carry some information about the
permeation process, and use more of the computer's time than yours (always
a good thing for a computational scientist).
Giacomo
On Fri, Jul 27, 2018 at 7:41 PM Jeff Comer <jeffcomer_at_gmail.com> wrote:
> Dear Kelly,
>
> If you are interested in the free energy along all five dimensions, you can
> usually do 1D ABF (which often helps with sampling along all degrees of
> freedom) and reweight to obtain PMFs along other directions. In this paper
> ( http://doi.org/10.1021/acs.jcim.7b00521 ), we generate a 3D PMF from a
> trajectory where ABF was applied along a single dimension. See equation 1--0000000000004f9cd4057207214c--
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