Re: is it possible to restrict the access of ions to certain volume?

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Mon Oct 31 2016 - 15:55:28 CDT

>>the easiest way would be to take note of the atom numbers of the ions you
want out of the pore, and use tclBC to force them out.

Thanks a lot for the idea! I did not think in this direction at all, will
try to implement this.

Olga

On Mon, Oct 31, 2016 at 4:43 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hello Olga,
>
> On Mon, Oct 31, 2016 at 4:28 PM, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>
>> Hi all,
>>
>> I am trying to figure out how to restrict the flow of ions into the
>> (narrow) channel for single-ion ABF calculations when the concentration of
>> ions is relatively high (i.e. it is certain that more than one ion will
>> enter the channel in the course of simulations).
>>
>> When I simulated the system with low concentration of ions I restrained
>> the ions at their positions with low force constant, but for high
>> concentration I do not think it's a good idea.
>>
>
> I don't think it's a good idea either way. Ions are supposed to diffuse
> around to contribute to the dielectric screening, even not counting that
> their initial position may not have been equilibrated.
>
>
>>
>> Ideally I would like to have some sort of exclusion sphere around the
>> tagged ion, but I did not find any discussions or descriptions of such a
>> thing. Is there a way to set up such a sphere in namd?
>>
>> Else, is it possible to apply distance/distanceZ/distanceXY in
>> combination in such a way that it would *exclude* the volume defined by
>> these colvars? For example, if I define a cylinder (as described in SMD
>> manual) and list all the ions except my tagged ion, can I limit their
>> motion to the outside of that cylinder somehow?
>>
>
> Yes, but the easiest way would be to take note of the atom numbers of the
> ions you want out of the pore, and use tclBC to force them out. Using
> Colvars instead could be a little tedious, since you would have to define a
> pair of cylindrical variables for each of the ions.
>
>
>
>>
>> Thanks in advance!!
>>
>> Olga
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
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>
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>
> *"As computer programmers we have a responsibility to make sure that we
> run the computers instead of the computers running us."* - Steve Oualline
>
>
>

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