Re: AW: moving out of the box

From: Ariel Talavera Perez (
Date: Fri Feb 14 2014 - 08:38:01 CST


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.


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

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