They are suggesting you to consider the periodic boundary conditions and to
center the system before calculating the RMSD.
On Sat, 2 Jun 2018, 3:38 a.m. Edjan Silva, <edjan.silva.esenfar.ufal.br>
wrote:
> 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?
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 01 2018 - 19:00:03 PDT
