VMD-L Mailing List

From: Steven Neumann (s.neumann08_at_gmail.com)
Date: Mon Oct 01 2012 - 05:56:33 CDT

thank you.

Shall I then save those coordinates in pdb and/or psf? - I mean is
that just a visual effect or when the box is shifted that means my
system is not in the box so the water will go to the vacuum while
running simulation?

Steve

On Mon, Oct 1, 2012 at 10:19 AM, Olaf Lenz <olenz_at_icp.uni-stuttgart.de> wrote:
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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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