From: Udaya Dahal (dahal.udaya_at_gmail.com)
Date: Mon Apr 01 2019 - 11:56:49 CDT
I actually found the solution after I submitted the question— the solution is in the wall boundary itself which I overlooked in previous reading. The wall actually uses half harmonic potential what I was looking for but I still need to implement it.
With regards to my previous simulation, I think you misunderstood what I did. Its not exactly periodic boundary wrapping (even though it is close to) and I am not simulating membrane but simple system where I need to see how the potential across the boundary is influenced by charge distribution. If there is non-neutral charge regions — it can create undesirable potential across the box and the result can be completely different from real systems. This is more for sanity check to make sure nothing unphysical (or unwanted ) is going on in the simulation.
> On Apr 1, 2019, at 12:49 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> wrote:
> Hi Udaya,
> Dumb question, but how are the ions allowed to move from one side of the membrane to the other? This sounds like they are wrapping across the periodic boundary, which probably isn't what you want. I terms of the applied forces, you know that you can use the tcl "expr" function to make complicated forces, right? This includes being able to impose harmonic potentials.
> On 2019-03-31 09:28:59-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
> Hi Everyone,
> I used TclBC forces to restrict ions to certain regions of a periodic box. Everything works exactly as it is supposed to work. One of the problem I face is the transition of ions from one region to the other, which I have to wait until next step to map it back using TclBC forces and this makes uneven charge distribution in those regions. Also, I wonder how the force on individual atoms are applied (for. eg. addforce "0 0 5"). It seems to me that we are applying force randomly to ions that transit from one region to another to map back it to its original location and may give rise to artifact (in an otherwise an equilibrium simulation) due to random forces.
> Instead I would like to use a wall to have a smooth potential function to restrict ions to the certain region like half parabola. I am wondering if it is possible to add such potential at the point of interest and for specific atoms only. If so, how can we implement this?
> I appreciate your help !
> Udaya Dahal
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