Re: system splitted

From: Aron Broom (
Date: Fri Mar 02 2012 - 09:21:12 CST

Hi Luis,

First, does the water box actually encompass all of the protein?

Second, the protein moving out of the box can't happen if you are using
periodic boundary conditions. So that means likely one of two things are

1) You didn't enable periodic boundary conditions and set the
cellbasisvector and other such needed parameters

2) Everything is fine, but namd wraps the protein as a whole rather than
just some of the atoms (I think that is the default maybe not), so what you
are seeing is a just a visualization issue (but in my opinion preferrable
to not wrapping). If this is true, you should be able to see on the
opposite side of where the protein appears to be "leaving the box" a void
space where there are no waters that would conveniently fit the portion of
the protein that appears to be outside the box.

In terms of your dimer splitting, or bad connectivity, I don't know, that
is something that requires more rigorous checking, you'll need to identify
exactly where the bad connectivity is first.


On Fri, Mar 2, 2012 at 7:54 AM, lecan <> wrote:

> Hi everybody.
> I am trying to minimize and MD simulate a protein in a water box with ions
> added with Meadionize plugin for VMD and charmm parameters. It minimizes to
> the end of the process apparently without trouble. At the first frame
> everything look OK, but at the second frame protein and water box split at
> the middle and move apart (is a dimeric protein). A part of each half of
> the protein moves out the half water box in which it is immersed and the
> connectivities of some residues are wrong. I have tried with a bigger water
> box, with the same result. Can anybody can give a light on this problem?
> Thank you in advance,
> Luis L.

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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