RE: TclBC forces on individual atoms

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Apr 01 2019 - 11:49:34 CDT

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.

-Josh

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 !
Thanks,
Udaya Dahal

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