VMD-L Mailing List

From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Sun May 25 2014 - 06:04:35 CDT

Hi!

2014-05-22 13:10 GMT+02:00 Norman Geist <norman.geist_at_uni-greifswald.de>:
>
> When you wrap a trajectory around a center of mass, this means that the
> image will move with the center of mass of the centersel. If you want an
>
>
>
> Yes, but why? If I move the com of centersel to the center of the unitcell
> and wrap, the box won’t move anymore. But VMDs pbc tools preserve this
> motion of
>
> Centersel what I can’t see any sense in context of centering.
>

The pbc tools never modify the coordinates of any atoms, but at most put
them into another periodic image. It might make sense to watch how the
center of mass of a selection moves, so the pbc tools do not remove it.
Getting rid of that move would be another operation.

image that does not move, you have to center around some absolute
> coordinates, e.g. the origin, or the center of the box.
>
>
>
> Yes, but I want to have the com of a centersel being in the middle of the
> pb without moving anymore.
>

Then you have to do that in an extra operation, by simply subracting the
center of mass from all atoms in the selection.

> The pbc methods do not rotate the system.
>
>
>
> I know, but RMSD align would, so it is not if an option to do the
> alignment after the wrapping.
>

Again, RMSD alignment is another operation than what the pbc tools do.

> It would be easy to script what I want, but as it will be used for a
> seminar, doing it with VMD build-in stuff would be of choice.
>

The pbc tools follow the Unix philosophy: they should do one thing only,
but do that correct. To get the overall effect that you want, you have to
combine different tools.
I think a script that does exactly these different steps would teach much
more than a single operation.

Olaf 

-- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607