Re: Multi-dimensional PMF

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Jul 27 2018 - 02:45:20 CDT

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> 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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