Keeping potassium ions out of an area during equilibration

From: Charles Hoying (
Date: Mon Jun 05 2017 - 22:57:40 CDT


I have a membrane protein that I want to equilibrate in NAMD without
allowing K ions from the solvation/ionization to get close to it.
Specifically, it has a pore with stable K+ binding sites on the outside, so
during equilibration before I run simulations I want to keep K+ ions away
from that pore.

I was thinking of modifying the "keep_water_out.tcl" script from the NAMD
Membrane Proteins Tutorial ( to recognize and keep
K+ ions out of the same region, but I don't know how. Specifically, I would
like to keep the ions out of the dimensions: (-3 < x < 3), (-3 < y < 3),
i.e. the pore axis.

I am open to any and all suggestions whether the script or some other
approach can help me solve the problem! Please let me know if there is
anything I can clarify to help answer my question.


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