Re: 1-D ABF and Compressibility

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jul 30 2018 - 16:14:56 CDT

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 <mcg05004_at_byui.edu> 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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