Re: AW: moving out of the box

From: Aron Broom (
Date: Fri Feb 14 2014 - 13:25:54 CST

yes I've seen that happen occasionally. You need to be very careful in the
options that you give PBC wrap.

Did you try the line that Normal recommended?

I would try first aligning all the frames using the RMSD trajectory tool
(it will not be confused by periodic boundaries the way our eyes are, and
will do everything correctly). Then use Normans line "pbc wrap -centersel
"protein or nucleic" -center com -compound residue -all

Does this still produce corrupted bonds?

On Fri, Feb 14, 2014 at 2:15 PM, Kenno Vanommeslaeghe <> wrote:

> You mean, like, after wrapping atoms around the periodic boundary, the
> bonds that cross the boundary seem to span the entire box?
> On 02/14/2014 09:38 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

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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