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

From: Olya Kravchenko (
Date: Tue Jun 28 2016 - 15:35:53 CDT

Hi Aron,

thank you for replying!

My system is ferritin, it is a spherical molecule that is empty inside
(such as soccer ball). The ions go inside through channels in the
surface, there are 8 channels, each consists of three chains. I am
trying to implement your suggestion now, i.e. align one of the
channels with Z axis.

For the harmonic restraint, what exactly should be restrained? I read
the manual about orientation variable, but I don't quite understand
what happens if I do not use it. The manual says it is needed to stop
the rotation of the protein. Why would it rotate?

Another thing: I recently ran a 20 ns simulation (I set it up without
PMF in mind at the time), so I now have a trajectory and roughly
identified ion pathway, but none of the channels are aligned with Z
axis. Do I understand it correctly that I cannot use the results for
obtaining PMF along the axis of the channel? Is there a conversion
that would allow me to utilize the current trajectory? (this is why I
thought about abscissa first).

Thank you,


On Sun, Jun 26, 2016 at 4:13 PM, Aron Broom <> wrote:
> 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 Z-axis.
> 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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