Re: restrict atoms to cross a boundary

From: Giacomo Fiorin (
Date: Mon Mar 04 2019 - 15:50:04 CST

Hi Udaya, the best option to apply an atom-by-atom boundary potential is
via TclBC. Colvars deals with average/total quantities, and defining a
separatevariable for every atom would be definitely tedious and inefficient.


On Mon, Mar 4, 2019 at 2:44 PM Udaya Dahal <> wrote:

> Hi Everyone,
> I am trying to restrict my ion flow to make specific part of a periodic
> box to be charge neutral
> Does the boundary potential wall in collective variable should be
> sufficient to create a wall only for ions between two chambers of a
> simulation box? To be more specific I need to put barrier in the middle of
> the box to restrict ions diffusion between to compartments. For that I will
> have* two sets of ions* to restrict to.
> Thank you !
> Udaya Dahal

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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