VMD-L Mailing List

From: Charles McCallum (mmccallum_at_pacific.edu)
Date: Thu Oct 27 2005 - 15:46:22 CDT

It turns out that what I suspected was correct --- that VMD will put
the axes at the *apparent" origin, not the global (0,0,0) origin.
On the one hand, I understand the utility of automagically centering
off-center coords, but perhaps the axes should really go at
the global (0,0,0), not the apparent....
Knowing how to check centers (thanks Marc!) helps.

Once I realized that and actually recentered the molecule, I got what
I wanted:

Cheers,

Mike

> hi charles,
>
> i would like to see why you got that behavior. did you check the
> coordinates of the center of the total system?
>
> measure center $all
>
> i am not sure if this gives you mass center or geometric center.
> assuming it is geometric center, it should be zero if you did as
> you said -- water box is centered at zero, and the molecule is
> centered inside the water box. Then after the pure rotation, the
> coordinates should remain unchanged -- only applied rotation.
>
> i doubt you have a perfect zero for geometric center. then you need
> to do
>
> $all moveby [vecinvert [measure center $all]]
>
> please let me know if this works ... and please keep this
> discussion off-line if it does not work :)
>
> cheers and have a good evening!
>
> Marc 

--
C. Michael McCallum           http://chemistry.cop.uop.edu/ 
cmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  /  
(209) 946-2607 fax
correct.jpg