Re: Multi-dimensional PMF

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Jul 27 2018 - 09:58:43 CDT

It's been a while since I've dealt with projections. Any suggestions on programs or the process you use to do that?

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: Friday, July 27, 2018 1:45:20 AM
To: Namd Mailing List; McGuire, Kelly
Subject: Re: namd-l: Multi-dimensional PMF

Hi Kelly,

the only way to plot 5D data is to project it into lower-dimension spaces. A 5D space is also difficult to sample. Typically we'll try to make our colvar space as low-dimension as possible, to make our life simpler.

Jerome

On Thu, 26 Jul 2018 at 23:43, McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

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

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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