VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 25 2010 - 08:35:22 CDT

On Tue, May 25, 2010 at 9:29 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> 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?

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_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.
> 

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