VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 25 2010 - 08:29:22 CDT

On Tue, May 25, 2010 at 9:25 AM, Hugo Gutierrez de Teran
<hugo.teran_at_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?

> 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_at_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_at_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_at_usc.es
> http://webspersoais.usc.es/persoais/hugo.teran/
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.