Centering alone probably won't be enough, because the RMSD routine does a
best-fit that will fix any centering problems. The more likely problem is
that your complex has been separated by periodic imaging. That's why I
suggested checking the archives for imaging, this has been discussed before
and you should find everything you need to fit it in the archives.
On Fri, Jun 1, 2018 at 10:35 AM, ABEL Stephane <Stephane.ABEL.cea.fr> wrote:
> Hi,
>
> You observed this behavior because you DNA-complex is not centered in the
> box. So you have to center the molecule in the box before to do the rmsd
> calculation
>
> HTH
>
> ________________________________________
> De : Edjan Silva [edjan.silva.esenfar.ufal.br]
> Envoyé : vendredi 1 juin 2018 16:26
> À : AMBER Mailing List
> Objet : [AMBER] high values ​​of RMSD during the simulation of molecular
> dynamics between DNA and small molecule. Does anyone explain?
>
> I performed a simulation between a small molecule and B-DNA. The result of
> the RMSD is this of the figure. By analyzing the structure at these points,
> it appears that some atoms get far away from the DNA, inside the box. Why
> does this happen? Does this make my simulation invalid?
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>
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Received on Fri Jun 01 2018 - 08:30:04 PDT
