Re: ABF with the RMSD colvar

From: George Patargias (
Date: Mon Sep 29 2014 - 05:25:01 CDT

Hello Jerome,

Many thanks for this comment. With a 2 ns free MD before an ABF window
all bins are now visited but I still get over-accumulation of samples in
the lower border. According to your paper there may be two potential
causes for this:

1) Too low force constant for upper/lower boundary (mine is 100


2) Too high Langevin damping gamma constant (mine is 5 ps-1)

I am not sure which one is more likely be the case.

> That's probably a major cause of your problems. ABF remains close to
> equilibrium, if all goes well, but if you start it away from equilibrium,
> that will cause trouble. Essentially, it will record non-equilibrium
> forces, and those will skew the biasing force and yield uneven sampling.
> Jerome

Dr. George Patargias
Postdoctoral Research Fellow
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27

Office: +302106597568

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