From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Tue Jun 28 2016 - 16:20:13 CDT
thanks a lot! I want to do both: set up a new simulation to obtain PMF
via ABF as well as analyze the one I already have. I just was not sure
if it is at all usable for PMF, particularly because I do not observe
ions leaving the channel (but I see progression through other binding
sites, they just get stuck at the last one).
On Tue, Jun 28, 2016 at 4:57 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> 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 <ovkrav_at_gmail.com> 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,
>> On Sun, Jun 26, 2016 at 4:13 PM, Aron Broom <broomsday_at_gmail.com> 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 <ovkrav_at_gmail.com>
>> > 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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