this RMSD plot was plotted after the use of the "cpptraj" command.
2018-06-01 22:20 GMT-03:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> I really think you should try the imaging commands in cpptraj. Autoimage is
> a good place to start.
>
> On Fri, Jun 1, 2018, 9:15 PM Edjan Silva <edjan.silva.esenfar.ufal.br>
> wrote:
>
> > 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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Received on Fri Jun 01 2018 - 19:00:03 PDT
