VMD-L Mailing List

From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Sat Apr 28 2007 - 13:27:51 CDT

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Hi!

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

Another simple approach would be to use the function "pbc wrap" like

        pbc wrap -center "resid b"

to wrap all atoms into a box centered around resid b, and use your
expression afterwards to select the residues.

Best regards

Olaf
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