VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun May 11 2008 - 10:54:53 CDT

Hi,
  We have a new "pbcwithin" command in the test builds of VMD 1.8.7
if you would like to try it, but the normal "within" command found
in older versions doesn't take PBC into account.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, May 11, 2008 at 12:04:57AM -0700, Neelanjana Sengupta wrote:
> Dear VMD users,
>
> Can anybody ascertain if the 'within' command takes into account periodic
> boundary conditions? In other words, for obtaining the atoms 'within' a
> certain distance of a selection, is the distance between the selection and
> each atom recalculated as:
> dx=dx - cell_a*NINT(dx/cell_a), etc?
>
> This is for a dcd file where the unit cell dimensions are specified at each
> step.
>
> Thanks,
> Neelanjana Sengupta
> -- 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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