VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon May 26 2014 - 02:20:27 CDT

 

Von: olaf.lenz_at_gmail.com [mailto:olaf.lenz_at_gmail.com] Im Auftrag von Olaf Lenz
Gesendet: Sonntag, 25. Mai 2014 13:05
An: Norman Geist
Cc: VMD Mailing List
Betreff: Re: vmd-l: pbc wrap -center com

 

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.

 

Or move the com of centersel to the cells center and wrap afterwards.

  

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.

 

Again, I know. It would have been the only VMD build in option for alignment, but not suitable here of course.

  

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.

 

Thats right, there are so much „center“ options and I just wondered that nobody ever needed such a option of translational alignment. Example a DX Volmap, which is scalar. I have a program that computes the temperature distribution through the cell and generate a DX file. The program has an option to align (translations only) a selection, for example a protein, to prevent of only seeing a kind of trace. To visualize this DX in VMD one needs to do the same centering which in fact is simple what I supposed the “pbc wrap –center com “ would do. But that wasn’t right. I wrote a little script that brings the com of centersel to the cell center before wrapping, and I’m fine with that so far.

 

I think a script that does exactly these different steps would teach much more than a single operation.

 

The students will never see that script, too less time to teach them in programming/scripting, too.

 

Thanks for your input

 

Norman

 

Olaf

  

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