Re: PMF with ABF for ion channels in a spherical molecule

From: Aron Broom (
Date: Sun Jun 26 2016 - 15:13:36 CDT

I don't think I fully understand what your system looks like.

But assuming it is some kind of continuous channel or pore, you can use the
DistanceZ collective variable, and align the channel along Z. Then you
would also use the Orientation collective variable with a harmonic
restraint to keep your spherical molecule's channel aligned with the

In terms of having a longer distance, that would depend. If you only cared
about being longer in one direction, you could define the reaction
coordinate as DistanceZ between the ion and the center of mass of atoms at
the channel entrance. If you wanted to get extra PMF information in both
directions, then I think you would need to use the dummy atom functionality
of the collective variable module to define a dummy atom at some particular
Z coordinate that would be before the channel entrance.

On Fri, Jun 24, 2016 at 6:01 PM, Olya Kravchenko <> wrote:

> 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.
> Olga

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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