Re: restrict atoms to cross a boundary

From: Udaya Dahal (dahal.udaya_at_gmail.com)
Date: Mon Mar 04 2019 - 15:59:57 CST

Thank you Giacomo !

On Mon, Mar 4, 2019 at 4:50 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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.
>
> Giacomo
>
> On Mon, Mar 4, 2019 at 2:44 PM Udaya Dahal <dahal.udaya_at_gmail.com> 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
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

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