Re: Unrealistically High Keq in eABF Seperation

From: Peter Freddolino (
Date: Wed Aug 25 2021 - 22:27:46 CDT

Dear Ishaan,
If your simulations haven't yet converged, there is really no sense in
evaluating the energies completely yet. With that said, how is the sampling
looking across the different values of your reaction coordinate? Is the
reaction coordinate stuck somewhere or is the system diffusing freely along
Have you visually inspected your system to make sure nothing weird is

On Tue, Aug 24, 2021 at 7:08 PM Ishaan Roy <> wrote:

> Hello,
> I am using eABF to separate two membrane proteins to find the free binding
> energy. The PMF values produced in my runs seem to be incredibly high
> compared to consistently reaching the 100s order of magnitude. We haven’t
> completed a run that plateaus in free energy yet, but this is an example
> showing what the PMF looks like.
> A maximum PMF this high already produces a value for the binding constant
> that is on an order beyond 10^100. Besides being high, it might be worth
> mentioning that the nonbonded energies are very close to 0 near the end of
> this run, but the PMF gradient doesn’t level off at all. Any ideas on what
> might be causing this? Or is such a value plausible? This only seems to be
> a problem with the separation runs; my other colvars produce PMF plots that
> are closer to what I’ve seen.
> Thanks,
> Ishaan


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