From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Jul 30 2018 - 14:44:53 CDT
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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