From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Sat Aug 15 2020 - 20:23:12 CDT
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: https://pubmed.ncbi.nlm.nih.gov/24081985/ I attach example tclBC inputs for comparison with yours.
On Aug 11, 2020, at 8:50 PM, Athreya, Nagendra Bala Murali <nathreya_at_illinois.edu<mailto:nathreya_at_illinois.edu>> 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:https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2015-2016/1610.html), 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.
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