From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jun 30 2021 - 20:52:49 CDT
Hi Ishaan, ABF or other adaptive biasing methods will try to overcome all
free energy barriers, including those preventing flipping. So flipping is
to be expected at some point, the question is whether the mechanism is
realistic and the associated energy as well. That depends on how big the
protein is, whether it's atomistic or CG, and a variety of other factors
that are specific to your project.
The upper limit and lower limit that you are using are the natural
boundaries of the tilt colvar: it makes sense to define a PMF in that
range. You didn't specify whether you also have walls at those locations,
but even if you did they would have no effect.
Giacomo
On Wed, Jun 30, 2021 at 9:45 PM Ishaan Roy <royi_at_uchicago.edu> wrote:
> Hi,
>
>
>
> I am running an ABF simulation on a membrane protein to find the binding
> free energy. In one of the systems, when running ABF on the tilt angle
> colvar, the protein flips over almost 180 degrees within the membrane.
> However, in other systems, the protein stays within a smell tilt angle
> range in the membrane when running the ABF on it. The tilt colvar currently
> has an upper and lower limit of 1 and -1. Could this problem be a result of
> the ABF countering interactions that would normally keep the protein in a
> natural orientation? If so, then to what values should the upper and lower
> limit be changed?
>
>
>
> Thanks,
>
> Ishaan
>
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