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

From: Olya Kravchenko (
Date: Mon Oct 31 2016 - 15:28:40 CDT

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.

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?

Thanks in advance!!


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