[gmx-users] ion flux counter

[Kutzner, Carsten]

> Am 26.09.2019 um 21:56 schrieb Harutyun Sahakyan <sahakyanhk at gmail.com>:
> 
> Hi Carsten,
> Thank you for replying,
> Is it possible to set CompEL for a non-double channel system? Without
> rising ions disbalance, just for counting.
Counting will only work properly if there are two compartments separated
by a bilayer, because the counting function makes sure that the ion
enters from one side and leaves to the other side. If it enters
and leaves on the same side, you don’t want to  count it as a permeation. 
With just a single bilayer and PBC, both sides 
of the channel belong to the same compartment.

Carsten


> I could use a piece of CompEL
> code to modify it for ion flux counting, maybe you have any suggestions?
> 
> Harut
> 
> On Thu, Sep 26, 2019 at 6:36 PM Kutzner, Carsten <ckutzne at gwdg.de> wrote:
> 
>> 
>> 
>>> Am 26.09.2019 um 16:24 schrieb Harutyun Sahakyan <sahakyanhk at gmail.com>:
>>> 
>>> Dear Gromacs users,
>>> 
>>> Computational electrophysiology protocol has some analyzing tools
>> allowing
>>> to count ion flux etc. I have used an external electric field to simulate
>>> the process of ion permissions through a membrane channel. How can I
>> count
>>> ion flux, conductivity or something like that?
>> If you are not using CompEL, which counts ion permeations on the fly,
>> I guess you have to write your own analysis scripts operating on the
>> trajectory.
>> 
>> Carsten
>> 
>> 
>>> 
>>> Best wishes,
>>> Harutyun Sahakyan
>>> Senior Assistant at Laboratory of
>>> Computational Modeling of Biological Processes,
>>> Institute of Molecular Biology, NAS, Armenia, Yerevan
>>> Tel: +374 93 323990
>>> h_sahakyan at mb.sci.am
>>> --
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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
>> 
>> --
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> 
> 
> -- 
> Harutyun Sahakyan
> Senior Assistant at Laboratory of
> Computational Modeling of Biological Processes,
> Institute of Molecular Biology, NAS, Armenia, Yerevan
> Tel: +374 93 323990
> h_sahakyan at mb.sci.am
> -- 
> Gromacs Users mailing list
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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