Re: ABF Window Boundaries

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Oct 19 2018 - 02:59:37 CDT

Hi Kelly,

First I would check the log file to see if your restraint parameters are
understood exactly the way you mean them by the Colvars module. Do you see
the diffusion out of the boundaries happen both in the colvars trajectory
and in the molecular trajectory as visualized in VMD? If there is an
inconsistency there, it could indicate a difference between how the value f
the variable is calculated and how you mean it.

Jerome

On Fri, 19 Oct 2018 at 09:48, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> In one of my ABF windows, the ligand moved outside the 3 angstrom window,
> even though I have lowerwallconstant and upperwallconstant set to 100.0
> kcal/mol. It never returned to the window, but diffused away. I have not
> seen that happen before. The other 9 ABF windows keep the ligand inside
> the window. Should I just increase the lowerwallconstant and
> upperwallconstant value, or should that have not happened with the value I
> used?
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
>

This archive was generated by hypermail 2.1.6 : Thu Sep 19 2019 - 23:20:00 CDT