Re: 1-D ABF and Compressibility

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Jul 30 2018 - 17:14:49 CDT

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: Jrme Hnin <jerome.henin_at_ibpc.fr>
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 <mcg05004_at_byui.edu<mailto: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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