Re: Cavernous Depressions in Water Box

From: Alex Balaeff (
Date: Sun Nov 22 2020 - 12:21:45 CST


There used to be an old bug in NAMD whereby an NPT simulation with
fixed atoms led to artifcats similar to those you described. Wonder if
that could be the case. If it is, my solution is to go with harmonic
restraints instead of outright fixing the atoms.



  Dr. Alexander Balaeff
  Polaris Quantum Biotech

On Sat, Nov 21, 2020 at 8:24 PM Oscar Bastidas <> wrote:
> Hello,
> 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 should:
> 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?
> Thanks.
> Oscar B.
> Oscar Bastidas, Ph.D.
> Postdoctoral Research Associate
> University of Minnesota

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