Not center, but to image. That's very different. Using cpptraj is not
enough, you must add the image command (or even easier, the autoimage
command) before you calculate rmsd.
On Fri, Jun 1, 2018, 9:57 PM Akash Deep Biswas <biswasakash95.gmail.com>
wrote:
> 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?
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Received on Sat Jun 02 2018 - 04:30:02 PDT
