Re: moving out of the box

From: Aaron Larsen (alarsen_at_molbio.mgh.harvard.edu)
Date: Thu Feb 13 2014 - 14:39:04 CST

Hi Ariel,

I am having trouble understanding exactly what you mean. Sometimes with
periodic boundary conditions set to on, it may appear that your biomolecule
is moving outside of the solvent box. It is usually not a problem at all
because the interactions with then solvent are still being modeled. Look at
the opposite face of the box and you may see a cavity in the solvent. This
indicates that the issue is one of visualization and not one concerning the
modelling of the solvent-biomolecule interaction.

Best,
Aaron

On Thu, Feb 13, 2014 at 3:31 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> 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
>
>
>

-- 
Aaron Larsen, Ph.D.
Harvard University Department of Chemistry and Chemical Biology
Harvard Medical School Department of Genetics
E-mail: alarsen_at_molbio.mgh.harvard.edu
Mobile: 617-319-3782
FAX: 617-643-3328

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