RE: shape change of water box and peptide move out

From: Michel Espinoza-Fonseca (
Date: Fri Jul 29 2005 - 12:35:09 CDT

As I used to do it before, I recommend you to go and take a look to the
tutorials. You can find one of them at:

It could help you to better run your simulations and to guide you better
to setup further simulations.

Finally, remember that peptides are very flexible, so you have to have
in mind that they will move very fast around the box, and eventually "go
out" of your box, and you'll see a "hole" on the other side of your box
(if you are using periodic boundary contidions). Don't get stressed,
it's just the "image" of you peptide.

-----Original Message-----
From: [] On
Behalf Of Dong Luo
Sent: Friday, July 29, 2005 12:10 PM
Subject: namd-l: shape change of water box and peptide move out

I have runned my peptide in period water box for
several times. Some were heat annealing processes. I
found sometimes the waterbox changed its shape and
holes appeared in it. Also part of the peptide moved
out from water from time to time. Without solid
background in molecular simulation, I dunno what it
means and weather it will make the results totally
nonsense. Any instructions or guide on reading
materials will be great appreciated.

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