From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Feb 13 2014 - 14:21:26 CST
In VMDs console
pbc wrap -all-compound res -center com -centersel "protein or nucleic"
or similar
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Ariel Talavera Perez
> Gesendet: Donnerstag, 13. Februar 2014 16:57
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: moving out of the box
>
> Hello,
>
> I just ran 0.5 us MD us of a protein dimer in complex with DNA in a
> water box. Unfortunately I did not restrain the neither the translation
> nor the rotation of the complex. In several frames part of the complex
> moved out of the water box. This makes that sometimes one of the
> monomers is gone from the water box, and the same monomer but from the
> neighbour cell appears.
> Is there anyway to fix this issue for the MD I already ran? I mean, how
> can I get the "right" complex in all the frames?
>
> Thanks a lot in advanced
>
> Cheers,
> Ariel
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