AW: cell origin problem

From: Norman Geist (
Date: Thu Sep 26 2013 - 00:59:57 CDT

Not only the protein sticks out, also everything else, what doesn't matter
as we do pbc ;)

I never used something different from origin 0 0 0 without expecting or
having any problems with it.


Norman Geist.


Von: [] Im Auftrag
von Haleh Abdizadeh
Gesendet: Mittwoch, 25. September 2013 21:01
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: namd-l: cell origin problem


Because of the periodic boundary condition? I mean a small part of protein
comes out of water box but i suppose it should enter the water box just next
to it. Am I right?


On Wed, Sep 25, 2013 at 8:44 AM, Norman Geist
<> wrote:

Nothing to worry about and no need to rerun the simulation.


Norman Geist.


Von: [] Im Auftrag
von Haleh Abdizadeh
Gesendet: Dienstag, 24. September 2013 16:53
Betreff: namd-l: cell origin problem


Dear all,

I have made a mistake in entering cell origin coordinates in restart conf
file. When I play the movie of trajectories I do not see any problem in my
protein but I am not sure if my results are correct or not. I know cell
origin is not the center of mass of the protein but center of the water box
so could anyone tell me if it is necessary for me to start the whole
simulation again?

Best wishes,



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