From: Axel Kohlmeyer (
Date: Fri Apr 27 2007 - 14:42:33 CDT

On Fri, 27 Apr 2007, Jianhui Tian wrote:

hi jinahui!

JT> Hi all,
JT> I am simulating a box of water using periodic condition with constant NPT.
JT> Here I want to get all the residue LIST of molecules within "x" of resid "b"
JT> by using "[atomselect top "within x of resid b"] get resid". If this
JT> molecule with resid "b" is on the edge of the unitcell, whether the LIST
JT> will contain the molecules whose periodic images are within the distance. If
JT> not? How can I do this? Thanks a lot.

this is a know problem and it is being worked on.

right now, one way to obtain the information you want directly
from VMD is to put corresponding copies of your system around the
principal box (i.e. 26 of them) and write the selection script, so
it only looks within the boundaries of the principal box.


JT> Jianhui

Axel Kohlmeyer
   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.