Re: What does "cellOrigin" really mean?

From: Alexandre A. Vakhrouchev (makaveli.lcf_at_gmail.com)
Date: Wed Apr 23 2008 - 08:36:51 CDT

Hi bo!

This parameter IS THE GEOMETRIC CENTER of your periodic system.
Corresponding vectors of the Cell show the size of box if it is
rectangular.

2008/4/23, bo liu <liubo.njuer_at_gmail.com>:
>
>
>
> 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
> VMD.
> And the periodic box turns out to be like pic1(attached). This seems odd
> anyway...
> 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!
>
> Yours
>
> --
> -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
>

-- 
Best regards,
Dr. Alexander Vakhrushev
Institute of Applied Mechanics
Dep. of Mech. and Phys.-Chem.
of heterogeneous mediums
UB of Russian Academy of Sciences
34 T. Baramzinoy St.
Izhevsk, Russia 426067
----------------------------------
С уважением,
    Вахрушев Александр Александрович
к.ф.-м.н., с.н.с.
Институт прикладной механики
Уральского Отделения
Российской Академии Наук
426067, г. Ижевск
ул. Т. Барамзиной 34
+7(3412)21-45-83

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