Re: moving out of the box

From: Ajasja Ljubetič (
Date: Thu Feb 13 2014 - 10:08:36 CST

Indeed there is. Depending on your needs, have a look at the
or the pbctools <>,
especially the "pbc wrap" command.

Best of luck,

On 13 February 2014 16:57, Ariel Talavera Perez <> 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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