Re: adaptive biasing force

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Oct 24 2018 - 16:00:02 CDT

The adaptive biasing force is applied to the collective variable that you
define in the Colvars configuration file. That is to say, it will be
applied to whatever atoms you've specified as group1 and group2 in this
file.

I don't know if "proteins pulled apart" is the right way to think about
ABF. When converged, the adaptive biasing force cancels the average
thermodynamic force intrinsic to the system. They diffuse apart by random
motion—there is no average pull one way or the other.

I'm note sure exactly how you are performing your calculation, but keep in
mind that it is very difficult to obtain adequate sampling and convergence
of the free energy for objects as large as two proteins. If you have a
reliable structure for the bound state, you can employ the methodology in
this paper: https://doi.org/10.1021/ct400273t

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us

On Wed, Oct 24, 2018 at 2:10 PM Artur Hermano <artur.hermano_at_hotmail.com>
wrote:

> Hello NAMD users,
>
> I am using the distance between two proteins as collective variable. I
> would like to know specifically where the adaptive force would act in each
> bin during an ABF simulation. I mean, in this case, how are the proteins
> pulled apart?
>
> Thank you very much!
>
> --
>
>
> Artur Hermano
>
>

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