Re: Simulating a system with an imaginary barrier

From: Giacomo Fiorin (
Date: Mon Aug 22 2022 - 04:35:03 CDT

Hi Monika, please try the tclBC option.


On Thu, Aug 18, 2022 at 3:54 PM Monika Kumari <> wrote:

> Dear all,
> I am trying to maintain an ion concentration gradient in a lipid
> membrane system. For this, I need to put an imaginary wall on one end of
> the box (restricting only the ions not water) so that the ions don't
> move to the other side via PBC. Also, the ions should move freely on one
> side of the membrane except for the restriction to cross the barrier.
> Can anyone suggest how to perform the simulation in NAMD?
> Thank you.
> Best regards,
> Monika

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