Re: Repulsive wall potential or spherical boundry conditions

From: Almeida-Hernández, Yasser, Dr. (
Date: Fri Oct 23 2020 - 12:58:25 CDT

Dear Giacomo,

Thank you very much for your reply. I will look at it.



From: Giacomo Fiorin <>
Sent: Friday, October 23, 2020 5:31:17 PM
To: NAMD list; Almeida-Hernández, Yasser, Dr.
Subject: Re: namd-l: Repulsive wall potential or spherical boundry conditions

Hello Yasser, look into either the documentation of TclBC or GridForces to implement a repulsive potential at custom boundaries for individual atoms. With the former, you need some familiarity with the Tcl scripting language, with the latter, you would need to prepare an OpenDX file containing the spherical boundary potential on a 3D grid.


On Fri, Oct 23, 2020 at 6:15 AM Almeida-Hernández, Yasser, Dr. <<>> wrote:

Dear all,

I am kinda new with restraints in NAMD.

My problem targets a water box, where those located at a certain radius from the system's COM are restrained/confined in a sphere of that radius. Diggin in the documentation I think this can maybe be done with a reflective/repulsive wall potential or spheric boundary conditions.

I would really appreciate it if someone guides me with an example or tutorial, like or similar to this problem.

Thanks in advance.



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