VMD-L Mailing List

From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Mon Oct 01 2012 - 04:19:32 CDT

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Hi!

On 10/01/2012 09:58 AM, Steven Neumann wrote:
> package require solvate solvate A_new.psf A_new.pdb -b 2 -minmax
> {{-10 -10 -10} {10 10 10}} -o Solv
>
>
> When I open pdb file Solv.pdb I see my protein solvated in the
> specified water box dimensions. however, when I type:
>
> pbc box
>
> The box boundaries are in a completely different place that my
> solvated system. How can I reset cooridante of my initial
> structure so that it will appear inside the pbc box?

The best in this case is probably to shift the box so that it fits.
Apparently, you box is centered around the origin, so

  pbc box -center origin

should do the trick. Otherwise play around with the other options of
"pbc box".

Olaf

- --
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
Phone: +49-711-685-63607
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