From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Aug 25 2020 - 19:27:34 CDT
You could try turning it off. I’m not sure that will make the difference, but I could be wrong. Other things to look at are the serials of the ions you want it to apply to (in the conf file) and perhaps also the range d over which the force is applied.
Best,
JC
> On Aug 25, 2020, at 4:06 PM, Athreya, Nagendra Bala Murali <nathreya_at_illinois.edu> wrote:
>
> 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 <mailto:gumbart_at_physics.gatech.edu>>
> Sent: Saturday, August 15, 2020 8:23 PM
> To: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>>; Athreya, Nagendra Bala Murali <nathreya_at_illinois.edu <mailto: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/ <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 <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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