VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jul 24 2009 - 09:17:13 CDT

On Fri, 2009-07-24 at 19:44 +0900, Linchen Gong wrote:
> Dear All,
>
> Could anyone please tell me whether "atomselect" takes into accout of
> the periodic boundary condition, if the cell size has been specified
> with "molinfo" command.

no.
the normal "within" keyword does not consider periodic boundaries.

VMD 1.8.7 will have a "pbwithin" keyword that serves this purpose.

cheers,
   axel.

>
> I want to label the water molecules within 3.3A distance to the
> protein, and find that one side of the protein is pretty close to the
> cell boundary. That is why I have this question.
>
> Thanks in advance
>
> Mark 

-- 
=======================================================================
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
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.