Cavernous Depressions in Water Box

From: Oscar Bastidas (
Date: Sat Nov 21 2020 - 19:22:14 CST


I've recently run a high salt (3X physiological conditions) NAMD simulation
on a large protein and the resultant production run trajectories show these
cavernous depressions on the water box - two bowl-like cavities, one cavity
on one face of the cube and the other on the opposite face.

I've looked up the phenomenon in the archived mailing list and no one there
has mentioned a high salt scenario like with what I'm working with here so
I'm not sure if my cause for the water box cavities is the same cause for
the archived event.

My collaborators and I are trying to decide how to remedy this whether we

1) Redo the simulation while fixing the protein's atoms so they don't move
and letting the waters fill in the cavities under a high temperature series
of NVT equilibration runs or if

2) We should use the grand canonical ensemble and add waters according to
the chemical potential if NAMD has an option for doing this.

Does anyone have any thoughts as to what happened to my high salt system
here and how we can address the cavities situation? Do the simulation
results for such cavities typically affect the simulation in aberrant ways
that wouldn't happen if the cavities weren't there?


Oscar B.

Oscar Bastidas, Ph.D.
Postdoctoral Research Associate
University of Minnesota

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