VMD-L Mailing List

From: Hugo Gutierrez de Teran (hugo.teran_at_usc.es)
Date: Tue May 25 2010 - 08:51:26 CDT

Axel,

Thanks again for the tips, you solved my problem!: I was loading a pdb file of the initial structure after the psf and before the dcd trajectory. Loading only the dcd after the psf did it.
I also upgraded to 1.8.7 to be on the safe side ;-)

Hugo

Axel Kohlmeyer wrote: 
On Tue, May 25, 2010 at 9:29 AM, Axel Kohlmeyer <akohlmey@gmail.com> wrote:
  
On Tue, May 25, 2010 at 9:25 AM, Hugo Gutierrez de Teran
<hugo.teran@usc.es> wrote:
    
I already tried pbc unwrap, but always get the same error:
"divide by zero"
      
that usually happens when you have a file without cell information.
are you by any chance loading a .pdb file on top of the .dcd?
    

or did you write an old style .dcd file, that has no cell information?
then you have to first load the cell dimention information for the .xst
file before you can use pbc unwrap (or wrap).

cheers,
   axel.

  
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
      
please upgrade of 1.8.7. there are many improvements
and bugfixes that went into 1.8.7, particularly in pbctools.

    
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/

      

--
Dr. Axel Kohlmeyer    akohlmey@gmail.com
http://sites.google.com/site/akohlmey/

Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

    



  


-- 
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/