From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Oct 19 2018 - 10:32:41 CDT
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<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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