VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 18 2006 - 17:08:27 CST

Lubos,
  I'd suggest having a look at the way the Solvate plugin works, as it
generates a solvent box by copying a template structure filling the required
space in much the same manner you'd like to replicate your periodic cell
into the other 26 neighboring locations. Solvate does this by building
structures with a combination of atom selections and psfgen. You can
basically replicate what solvate does and tune it for your particular needs.
You can either get the solvate script from the plugins directory of your
VMD installation, or via CVS from the VMD web site:
  http://www.ks.uiuc.edu/Research/vmd/doxygen/cvsget.html#cvsget

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 18, 2006 at 03:08:41PM +0100, Mgr. Lubos Vrbka wrote:
> hi guys,
>
> i asked already once but didn't get any replies, so i'm trying it once more.
>
> i need to create all 26 periodic images of a set of atoms, or better to
> say, i need to create all 26 periodic images surrounding a simulation
> box. is there a way how to do that?
>
> what do i need it for? i need to count the number of hydrogen bonds
> every molecule forms with its neighbors. the problem is that the
> respective commands in the vmd (measure hbons, for example) are not PBC
> enabled. so creating all periodic images of the central simulation box
> is one of the ways how to treat it.
>
> it should then work like:
> for N in central_box
> for M in central_box_and_all_replicas
> measure hbonds of N with M
>
> i would be really glad if someone could help me. i tried to have a look
> in the manual, but nothing seems to be appropriate for this task. (doing
> this analysis for every frame in the trajectory should be the easy part
> of the task)
>
> thanks,
> lubos
>
> --
> .....................................................
> Mgr. Lubos Vrbka
>
> Center for Biomolecules and Complex Molecular Systems
> Institute of Organic Chemistry and Biochemistry
> Academy of Sciences of the Czech Republic
> Prague, Czech Republic
>
> http://www.molecular.cz/~vrbka
> ..................................................... 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078