VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jun 27 2008 - 12:51:26 CDT

On Fri, 27 Jun 2008, dimka wrote:

DK> Hi VMD list, can you please tell me how to select a cylindrical volume?
DK>
DK> i've tried something like this but it doesn't work
DK>
DK> "within 10 of (x==0 and y==0)"
DK>
DK> supposedly this command should select a cylindrical slab in the Z

who said that it should?

DK> direction... but it doesn't.

of course it does not work. don't think that a computer program
does something reasonable, but you'll have to follow the logic.

(x==0 and y==0) would select only particles that have the x-coordinate
and y-coordinate to be exactly 0. that is highly unlikely
and within would select sphere around it anyways. what you need is
something like

sqrt(x*x + y*x) < 10.0

or if you want the cylinder around x=2 and y=-3:

sqrt((x-2)*(x-2) + (y+3)*(y+3)) < 10.0

think about it for a bit and it will become evident. ;-)

cheers,
  axel.

DK> 

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