VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 14 2005 - 11:29:42 CST

Lubos,
  At present, VMD's atom selection language ignores PBC and only
does calculations against the loaded coordinates. We are interested
in extending VMD to include such functionality, but it isn't available
yet. In order to do this type of calculation presently, you'd need to
do custom scripting. Some people have written such scripts already,
so it's doable, though we'd like to add some of the low-level calculations
into VMD so that the heavy lifting isn't being done via scripting languages.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 14, 2005 at 05:29:45PM +0100, Mgr. Lubos Vrbka wrote:
> hi,
>
> i have one more question, this time regarding the display (and analysis)
> of structures with Periodic Boundary Conditions. if i load such a
> structure (e.g. amber trajectory) to amber and specify
> within 10 of (resid X)
> i get perfect results for "resid X" located in the center of the box.
> however, when "resid X" is close to the box boundary, PBS conditions are
> not taken into account, i.e. residues in larger distance than 1/2 of the
> box are not (correctly) reported as fulfilling the condition.
> i suspect that "measure contacts" command works in the same way like
> "within" selection macro (however i haven't tested that). this would
> result in incorrect (smaller) number of contacts reported for residues
> near the box boundary.
>
> i know that easy way of treating such problem might be imaging of the
> trajectory, but even this procedure may fail on some special occasion.
> however, i do it for proteins now. for salt solution, i would have to
> image the trajectory for every single ion in the unit cell...
> is there any way how to address this problem?
>
> thank you for hints. with best regards
> lubos
>
> --
> .....................................................
> Mgr. Lubos Vrbka
>
> Center for Complex Molecular Systems and Biomolecules
> Institute of Organic Chemistry and Biochemistry
> Academy of Sciences of the Czech Republic
> Prague, Czech Republic
> ..................................................... 

-- 
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