Re: ABF Window Boundaries

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Oct 19 2018 - 10:35:27 CDT

https://raw.githubusercontent.com/Colvars/colvars/master/colvartools/plot_colvars_traj.py

On Fri, Oct 19, 2018 at 11:34 AM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> I checked the molecular trajectory in VMD and the ligand does, indeed,
> diffuse away. I've never checked the colvars trajectory before, how do I
> do that? Thanks!
>
>
> *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*
>
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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