VMD-L Mailing List

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Mon Apr 30 2007 - 15:57:30 CDT

Hi Olaf,

How to add the pbctools plugin into my vmd-1.8.5 version on Linux after I
got the tcl script from
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbctools/. Thanks
a lot.

Jianhui

On 4/28/07, Olaf Lenz <olenz_at_fias.uni-frankfurt.de> wrote:
>
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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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