Re: ABF Window Boundaries

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Oct 19 2018 - 10:34:38 CDT

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: Jrme Hnin <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<mailto: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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