Thanks a lot for the help. The problem may be with the input file settings.
configurations of a protein - drug simulation were used, with few
alterations. maybe this is the problem.
2018-06-01 12:17 GMT-03:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> 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 - 18:30:03 PDT
