From: Athreya, Nagendra Bala Murali (nathreya_at_illinois.edu)
Date: Tue Aug 25 2020 - 15:06:12 CDT
Hey JC,
Thank you for the helping me out. Sorry for the delayed response as I was trying to run couple to simulations to test various things to fix the issue, which turned out to be unsuccessful.
I had previously tried to replicate similar system as mentioned in your publication with a 2D membrane. I used the script you provided to restrict the ions to maintain asymmetric concentrations (10mM:1M), however, I just observe the ions wrapping around z-coordinate and making a symmetric concentration across the membrane. I also tried the adjust the ratios in the script for K+ and Cl- ions, even this did not work.
Should I use "wrapAll off"? (in your config file, it is still kept on).
Thanks,
Nagendra
________________________________
From: Gumbart, JC <gumbart_at_physics.gatech.edu>
Sent: Saturday, August 15, 2020 8:23 PM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Athreya, Nagendra Bala Murali <nathreya_at_illinois.edu>
Subject: Re: namd-l: Asymmetric concentration gradient: non-periodic z-boundary for only ions
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: https://pubmed.ncbi.nlm.nih.gov/24081985/ I attach example tclBC inputs for comparison with yours.
Best,
JC
On Aug 11, 2020, at 8:50 PM, Athreya, Nagendra Bala Murali <nathreya_at_illinois.edu<mailto:nathreya_at_illinois.edu>> wrote:
Hi,
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.
Thank you,
Nagendra
<1V.namd><eq.namd><min.namd><z_BC.tcl>
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