VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Jun 04 2018 - 09:35:28 CDT

Yes, sorry about that. After sending those ABF questions, I remembered there was an NAMD forum.

Kelly L. McGuire
PhD Scholar
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602

________________________________
From: Jérôme Hénin <jerome.henin_at_ibpc.fr>
Sent: Monday, June 4, 2018 6:26:33 AM
To: McGuire, Kelly
Cc: VMD Mailing LIst
Subject: Re: vmd-l: PMF Question

Hi Kelly,

this is really a NAMD question, please use the NAMD list for this. That said, the boundaries you provide are those of the grid that is used to estimate the PMF: nothing is computed outside of those.

Jerome

On 31 May 2018 at 20:39, McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:
In ABF, is the PMF calculated if the molecule strays outside of the lowerboundary and upperboundary window? Say LB is 2 and UB is 4, and the molecule diffuses outside of that 2 and 4 window, what happens to the PMF calculations? Thanks!

Kelly L. McGuire
PhD Scholar
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602