Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions

From: Gumbart, JC (
Date: Sat Aug 15 2020 - 20:23:12 CDT

Hi Nagendra,

The ions spreading out is just a visualization artifact of them no longer being wrapped. The problem, I think, is in your tcl bc script. Try using "wrapmode cell”.

We did something similar to what you want to do in this paper: I attach example tclBC inputs for comparison with yours.


On Aug 11, 2020, at 8:50 PM, Athreya, Nagendra Bala Murali <<>> wrote:


I am trying to simulate an ion channel under electric bias with asymmetric concentration gradient conditions (where X,Y-directions can be periodic, however Z-direction needs to be non-periodic for ions). The ions on one side of the channel is 10mM and the other side is 1M.

When I tried to simulate with PBC (using wrapAll = ON), the ions move to the other side and the whole system neutralizes over time.

When I turn wrapAll OFF, and use a tclBC script to push ions from the z-boundaries (as suggested here:, the ions just expand in all directions but everything else remains in the initial defined cuboid.

I am not sure what is going on. I have attached the minimization, equilibration, and script when voltage is applied. Am I missing something?

I would appreciate any help I can get.

Thank you,

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