What does "cellOrigin" really mean?

From: bo liu (liubo.njuer_at_gmail.com)
Date: Fri Apr 18 2008 - 09:38:56 CDT

Hi all users

I am bogged down by a common concept in NAMD: cellOrigin.

I set the cellOrigin to be the center(measure center) of my system as the
tutorial does.
After the simulation completed, i used pbctools to load the .xst file into
And the periodic box turns out to be like pic1(attached). This seems odd
I suppose the cell box should wrap the system in most cases and the
cellOrigin should be
the center of periodic cell as the manual indicates.

However, my experiment shows that the cellOrigin actually means the origin
of cell basis vectors?

Maybe I have misunderstand what the "cellOrigin" really means... NEED HELP!

Regards and Many Thanks!


-Liu bo
Computational Biology, Nano-bio systems: MD method;
College of Chemistry and Chemical Engineering, Graduate University of
Chinese Academy of Sciences, Beijing P.R. China
Office: (86)-010-88233187
Home: (86)-010-88259765
Cell: 13426057875


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