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

From: Aron Broom (
Date: Tue Jun 28 2016 - 15:57:14 CDT

Hi Olga,

For the orientation restraint, the protein will rotate just because of
random thermal motion and interaction with the solvent.

I had thought you were thinking of setting up some kind of biased
simulation, like umbrella sampling, adaptive bias force, or something
else. But it sounds like you just want to do the analysis of an existing
simulation. In that case no restraints are needed.

If you think that you have something useful in your 20 ns simulation and
you are hoping to just analyze it along a single reaction coordinate to
generate a PMF, then I think you could just use the distance from the ion
to the center of mass of the whole ferritin.

I have never done ion transport simulations, but I would be surprised if 20
ns was long enough to see enough transits to get good statistics for a PMF.


On Tue, Jun 28, 2016 at 4:35 PM, Olya Kravchenko <> wrote:

> 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,
> Olga
> 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

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

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