VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jun 04 2018 - 07:26:33 CDT

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> 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
>