From: George Patargias (gpat_at_bioacademy.gr)
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
kcal/mol/Ang^2)
or/and
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
Athens
Greece
Office: +302106597568
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:53 CST