VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun May 11 2008 - 03:35:53 CDT

On Sun, 11 May 2008, Neelanjana Sengupta wrote:

NS> Dear VMD users,
NS>
NS> Can anybody ascertain if the 'within' command takes into account periodic
NS> boundary conditions? In other words, for obtaining the atoms 'within' a
NS> certain distance of a selection, is the distance between the selection and
NS> each atom recalculated as:
NS> dx=dx - cell_a*NINT(dx/cell_a), etc?

no. 'within' does _not_ take PBC into account.

proper PBC support is high on many people's TODO lists,
but it is not a simple to implement without sacrificing
too much performance for the 'normal', non-pbc case.

cheers,
    axel.

NS>
NS> This is for a dcd file where the unit cell dimensions are specified at each
NS> step.
NS>
NS> Thanks,
NS> Neelanjana Sengupta
NS> --
NS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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