[gmx-users] Analysing multiple cavities in ion Channel through CompEl simulations

[Kutzner, Carsten]

Hi Carlos,

> Am 20.08.2019 um 13:12 schrieb Carlos Navarro <carlos.navarro87 at gmail.com>:
> 
> Dear gmx-users,
> I'm currently investigating ion permeability in a channel that displays
> multiple cavities through ComEl simulations. Unfortunately one can just
> define a single cylinder per membrane.
Yes, this counting of ion permeations on the fly is just a convenience
function for the most common use case of a single pore per channel.
However, everything can be extracted from the output trajectory,
given that the time gaps between the trajectory frames are not too long.

> Considering the size of my system
> (>440k atoms) I don't think is a viable idea to run n independent
> simulations for the n cavities want to study, so I guess my only choice is
> to run a single simulation creating a big cylinder that comprises all the
If you need to script something that keeps track of the ion movements,
you don’t even need that big cylinder, as it will only tell you which ions
go through the upper and which go through the lower channel. But maybe
that information facilitates things a bit.

> cavities, and then by scripting check from which cavity the different ions
> are passing. What do you think about this approach? I'm open to suggestions.
If you don’t want to do too much scripting, you could easily output the
position of each permeating ion directly after the permeation has finished.
This should allow you to tell through which of several pores each ion has
permeated. 

If you don’t mind to code a little bit, have a look at detect_flux_per_channel() 
in swapcoords.cpp. Look for line „Atom nr. %d finished passing %s“. You
could output the ion’s position as well (atomposition[x/y/z]) to know 
where it has left the channel. You might need an xy position
restraint on the centers of mass of the channels for easier interpretation
(but it should work without a restraint as well, just with some more effort 
on the scripting side).

Best,
  Carsten


> Best regards.
> Carlos
> 
> ----------
> 
> Carlos Navarro Retamal
> 
> Bioinformatic Engineering. PhD
> 
> Postdoctoral Researcher in Center for Bioinformatics and Molecular
> Simulations
> 
> Universidad de Talca
> 
> Av. Lircay S/N, Talca, Chile
> 
> T: (+56) 712201 <//T:%20(+56)%20712201> 798
> 
> E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa