VMD-L Mailing List

From: Hugo Gutierrez de Teran (hugo.teran_at_usc.es)
Date: Tue May 25 2010 - 08:25:37 CDT

I already tried pbc unwrap, but always get the same error:
"divide by zero"
I have been checking for a while before posting, but really found no tip about this particular problem.

Thanks for your answer,
Hugo

PS: vmd 1.8.6 on a linux box
Axel Kohlmeyer wrote: 
2010/5/25 Hugo Gutiérrez de Teran <hugo.teran@usc.es>:
  
Hi,

I have a MD simulation (dcd file) created with NAMD, using options -wrap
on. The protein is a dimer, and the problem in the visualization and
analysis is that often one monoper croses the PBC cell and appears on
the other side, while the other monomer remains in the original cell.
I tryed to align the protein with "align" command in RMSD trajectory
tool, but only subunit A remains unchanged, while subunit B fluctuates
between one or other side of the cell. This way I can not analyze the
RMSD or the interactions between proteins.
Any ideas?
    

how about using "pbc unwrap" in VMD?

check the mailing list archives. this is a common problem
and there should be a lot of discussions and suggestions
on the subject.

cheers,
    axel.

  
Hugo

--
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundación Pública Galega de Medicina Xenómica - SERGAS
Santiago de Compostela (SPAIN)

Phone +34 981563100 ext 13873
e-mail:hugo.teran@usc.es
http://webspersoais.usc.es/persoais/hugo.teran/


    



  


-- 
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundación Pública Galega de Medicina Xenómica - SERGAS
Santiago de Compostela (SPAIN) 

Phone +34 981563100 ext 13873
e-mail:hugo.teran@usc.es       
http://webspersoais.usc.es/persoais/hugo.teran/