Free Energy Calculations on Helical Dimer: Separation Run Snaps Back

From: Ethan Croitoru (
Date: Sun Apr 18 2021 - 15:26:27 CDT


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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