Re: AW: moving out of the box

From: Aaron Larsen (alarsen_at_molbio.mgh.harvard.edu)
Date: Fri Feb 14 2014 - 09:10:36 CST

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

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 <atalaver_at_vub.ac.be>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: 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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