VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu May 22 2014 - 06:10:23 CDT

 

Von: olaf.lenz_at_gmail.com [mailto:olaf.lenz_at_gmail.com] Im Auftrag von Olaf Lenz
Gesendet: Donnerstag, 22. Mai 2014 12:45
An: Norman Geist
Cc: VMD Mailing List
Betreff: Re: vmd-l: pbc wrap -center com

 

Hi!

 

Can you try to restate your question? I do not fully understand it.

 

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.

 

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.

 

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.

 

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.

 

Thanks

 

Olaf

 

2014-05-22 11:43 GMT+02:00 Norman Geist <norman.geist_at_uni-greifswald.de>:

Hi,

 

is there any special reason why the „box“ is still moving after having wrapped with “–center com –centersel whatever” or otherwise, is there an option to align a system by just translations _not_ rotations or will I have to script that?

 

Thanks

 

Norman Geist

 

  _____

 <http://www.avast.com/>

Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus <http://www.avast.com/> Schutz ist aktiv.

 

  

-- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607
---
Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.
http://www.avast.com