Re: Free Energy Calculations on Helical Dimer: Separation Run Snaps Back

From: Jérôme Hénin (
Date: Mon Apr 19 2021 - 11:04:49 CDT

Hi Ethan,

Fluctuations are always possible in ABF calculations (that's the point of ABF, really). 5 ns is not an unreasonable timescale for that to happen. Unless you see something else that looks pathological, I would not worry about that.


----- On Apr 18, 2021, at 10:26 PM, Ethan Croitoru <> wrote:

> Hello,
> I am calculating the free energy of binding between a helical dimer following
> the protein ligand binding tutorial. When I run the simulations to calculate
> the contribution of separation I set the upperboundary to 40A, and I run this
> for 40ns (split into 2 20ns runs). At the beginning of the second run the dimer
> reached the 40A and very quickly snapped back together to about 13A (their
> starting distance). It took about 23 ns to pull apart the dimer, but it snapped
> back within 5ns. I was wondering what was occurring here because I thought the
> upperboundary parameter did not affect dynamics and only affected the bins for
> ABF calculations. Any insights would be appreciated.

> Thank you,
> Ethan Croitoru

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