PMF with ABF for ion channels in a spherical molecule

From: Olya Kravchenko (
Date: Fri Jun 24 2016 - 17:01:13 CDT

Hi all,

I am trying to figure out how to calculate PMF for ion channels in a
spherical molecule. I would like to use position of the ion along the
channel axis as the reaction coordinate. How does one define the
reaction coordinate for a radial channel in a sphere?

At this moment I can only think of defining it via abscissa and use
centers of mass of the atoms at the entrance and exit of the channel.
But then residues there move, would that affect the reaction
coordinate? Also, if I want the distance to be longer than the length
of the channel, how would I define that within abscissa?

I would appreciate your input.


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