Multi-dimensional PMF

From: McGuire, Kelly (
Date: Thu Jul 26 2018 - 16:40:28 CDT

So, everything seems to be working having a distanceZ colvar and 4 dihedral colvars (to bias the 4 histidine sidechains in my ion channel). But, now that means I have a 5-D .grad and .count, instead of just the 1-D .grad and .count which writes a 1-D PMF. I know how to use abf_integrate and got that to work to create a PMF. But, we are wondering how to even begin plotting data beyond 1, 2, and 3-D...

The reason I am biasing those four dihedrals is because our 1-D PMF was skewed, meaning bulk water on the c-terminus side of the ion channel is 30-50 kcal/mol higher than bulk water on the n-terminus side (they should be the same energy). We believe this energy value corruption is due to these histidines, so we are biasing them. We would like to see if this fixed the corrupted energy values on the 1-D PMF, how would we go about doing that?

Kelly L. McGuire

PhD Scholar


Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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