From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Feb 13 2014 - 10:08:36 CST
Indeed there is. Depending on your needs, have a look at the
fitframes<http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/fitframes/>
script
or the pbctools <http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/>,
especially the "pbc wrap" command.
Best of luck,
Ajasja
On 13 February 2014 16:57, Ariel Talavera Perez <atalaver_at_vub.ac.be> wrote:
> 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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