Re: ABF Window Boundaries

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Sun Oct 21 2018 - 17:28:15 CDT

This probably means that the ligand has diffused across the PBC unit cell
boundary with respect to the receptor, so the minimum-image distance
remains small. You can check that by wrapping the coordinates in VMD around
the receptor.

Jerome

On Fri, 19 Oct 2018 at 17:35, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> Nevermind on that last question. The colvars trajectory shows that the
> ligand is within the specified 3 angstrom window, so there is a discrepancy
> between the molecular trajectory and the colvars trajectory. What causes
> that?
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> ------------------------------
> *From:* Jérôme Hénin <jerome.henin_at_ibpc.fr>
> *Sent:* Friday, October 19, 2018 1:59:37 AM
> *To:* Namd Mailing List; McGuire, Kelly
> *Subject:* Re: namd-l: ABF Window Boundaries
>
> 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*
>
>
>

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