Re: AW: moving out of the box

From: Aaron Larsen (
Date: Fri Feb 14 2014 - 09:10:36 CST

"the structure is completely corrupted with very bad bond distances in some

This may have had something to do with the step in which you made your psf
file. I would suggest loading the .psf and .pdb files you are using for the
minimization/production runs and verifying that the structures look fine.

On Fri, Feb 14, 2014 at 9:48 AM, Ariel Talavera Perez <>wrote:

> Hi
> First of all. Thanks to all for the quick answers.
> So far I managed to always get the DNA and the protein dimer in all the
> frames. Although, the structure is completely corrupted with very bad bond
> distances in some frames.
> Cheers,
> Ariel
> 14 09:21 PM, Norman Geist wrote:
>> In VMDs console
>> pbc wrap -all-compound res -center com -centersel "protein or nucleic"
>> or similar
>> Norman Geist.
>> -----Ursprüngliche Nachricht-----
>>> Von: [] Im
>>> Auftrag von Ariel Talavera Perez
>>> Gesendet: Donnerstag, 13. Februar 2014 16:57
>>> An:
>>> 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
Mobile: 617-319-3782
FAX: 617-643-3328

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