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

From: Giacomo Fiorin (
Date: Mon Oct 31 2016 - 15:43:34 CDT

Hello Olga,

On Mon, Oct 31, 2016 at 4:28 PM, Olya Kravchenko <> 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
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
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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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