AW: system splitted

From: Norman Geist (
Date: Mon Mar 05 2012 - 00:59:23 CST



I think Aron is right. It is just a visualization issue. You should better
remove the option WrapAll from your script and look at the pbc tools plugin
in vmd to wrap the coordinates by your needs. Regarding the wrong bonds I
think you loaded the pdb instead of psf. Vmd needs to know your topology to
show the right properties of your molecule, so don’t load the dcd into the
pdb, as the pdb doesn’t have any reliable information on bonding etc., but
the psf has all that information. So 1st load the psf and the dcd into it
and look if the bonds remain wrong, but I guess it’s ok then. Note that
bonding of a pdb file is determined by distances, what is told to you by


Norman Geist.


Von: [] Im Auftrag
von Aron Broom
Gesendet: Freitag, 2. März 2012 16:21
An: lecan
Betreff: Re: namd-l: system splitted


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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