is there a way to prevent ions from entering the channel?

From: Olya Kravchenko (
Date: Thu Jul 21 2016 - 12:56:57 CDT

Hi all,

I am trying to calculate PMF in the ion channel, and for this I would
like to keep the channel free of other ions. I can manually remove the
ions after each round of simulations, but I wonder if there is a
simple way to prevent other ions from approaching the tagged ion
within certain distance, or maybe bouncing off from the entrance of
the channel (and without affecting the PMF)? It is a narrow channel,
so there are usually no more than 3 ions there at once, and in
principle manual removal is not a problem, but I wonder if there is
more efficient or more correct way to do this.

I would very much appreciate your help!


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