Re: Cavernous Depressions in Water Box

From: Peter Freddolino (
Date: Sat Nov 21 2020 - 21:14:01 CST

Dear Oscar,
an important general question to ask yourself is, does this simulation
behavior match what you'd expect in the real system? Almost assuredly not,
which means it is a problem that needs to be addressed. As you've inferred,
in general it seems that your simulation doesn't have enough solvent given
all other characteristics of the system. We would need a bit more
information to give good advice though, notably including:
-how did you solvate the system?
-what ensemble are you running in? (this is crucial. A constant pressure
simulation should not allow the formation of the type of cavity that you
describe unless there are some constraints on the system or there is a
region of the system that is topologically isolated from the rest -- you
can see behavior like this, for example if you don't sufficiently solvate
the interior of a simulation containing a viral capsid)
-are there any other simulation features being used besides a standard md


On Sat, Nov 21, 2020 at 9:08 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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