VMD-L Mailing List

From: Matt Watkins (ucapmw0_at_ucl.ac.uk)
Date: Wed Mar 26 2008 - 17:07:58 CDT

Yes, thanks that works beautifully. So all you materials chemistry type
people use 'pbc wrap -nocompound ...'

Cheers,

Matt

Axel Kohlmeyer wrote:
> On Wed, 26 Mar 2008, Matt Watkins wrote:
>
> MW> Hi all,
> MW>
> MW> I've been struggling to use the pbc tools plugin on a system I'm trying to
> MW> analyse. I want to center the view on "index 1471", but the command
> MW>
> MW> pbc wrap -center "index 1471"
> MW>
> MW> is either producing strange results or naught. This occurs for vmd.1.8.6 or
> MW> the latest alpha(as of today).
>
> matt,
>
> that is probably because of the default of pbctools to wrap by
> residue. i guess you want a wrap by atom, right? try:
>
> pbc wrap -nocompound -center "index 1471"
>
> ...and then you probably need to recompute the bonds with:
>
> mol bondsrecalc 0
>
> hope this helps,
> axel.
>
> MW> The file is problem.xyz.bz2 uploaded to biocore. It contains the cell
> MW> parameters in the second line, which I was setting with
> MW>
> MW> pbc set { 26.92 31.08 59.30 }
> MW>
> MW> originally the file was a dlpoly_history2 file that after experiencing
> MW> similar problems, I converted to xyz...if that can make any odds.
> MW> ,
> MW> cheers,
> MW>
> MW> Matt
> MW>
>