Re: 1-D ABF and Compressibility

From: Jérôme Hénin (
Date: Tue Jul 31 2018 - 00:43:50 CDT

Look at it this way: if the constriction didn't result in forces along z,
it would not hinder motion along z.


On Tue, 31 Jul 2018 at 00:15, McGuire, Kelly <> wrote:

> Ok great that simplifies life quite a bit. We would like to understand
> that a bit more, is there some reference to constriction and the forces
> produced? I'm sure studying the physics and vectors will help us with that,
> but maybe a text or paper that goes over that with proteins and biological
> systems would help. Thanks!
> Kelly L. McGuire
> PhD Scholar
> Biophysics
> Department of Physiology and Developmental Biology
> Brigham Young University
> LSB 3050
> Provo, UT 84602
> ------------------------------
> *From:* Jérôme Hénin <>
> *Sent:* Monday, July 30, 2018 3:14:56 PM
> *To:* Namd Mailing List; McGuire, Kelly
> *Subject:* Re: namd-l: 1-D ABF and Compressibility
> Actually a channel constriction in xy will result in forces along the z
> direction as well, which will enter the average and be accounted for by
> ABF.
> Jerome
> On Mon, 30 Jul 2018 at 21:48, McGuire, Kelly <> wrote:
> We have a question about the distanceZ colvar and 1-D ABF. I was reading
> the The Adaptive Biasing Force Method: Everything You Always Wanted To
> Know but Were Afraid To Ask paper and the colvars guide, but couldn't
> answer this question:
> If we have a 1-D reaction coordinate set up using distanceZ for our ABF,
> are forces from the x and y directions in a channel included in the PMF?
> For example, if there is a region of sidechains that would create a barrier
> to drug entry, which would be a compressible region in the channel, would
> the forces coming from the x and y directions be projected or calculated in
> this 1-D PMF, thus contributing to the barriers energy height, or is the
> barrier height being underestimated by the ABF because those compressible
> forces (i.e. channel/sidechains squeezing the drug) aren't being considered
> in that barrier's energy calculation?
> Would we need to include a distanceXY colvar and go to 2-D to get a more
> accurate barrier energy calculation to include compression (or stretching)
> of the channel as the samples in those types of regions?
> *Kelly L. McGuire*
> *PhD Scholar*
> *Biophysics*
> *Department of Physiology and Developmental Biology*
> *Brigham Young University*
> *LSB 3050*
> *Provo, UT 84602*

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