Hi Nada,
You shouldn’t expect your trajectories to be continuous with respect to
RMSD, if they are three independent trajectories. Unless you ran 1
trajectory, and started the next trajectory from trajectory 1’s restart
file, the atom positions are not going to be conserved and hence your plot
will have jumps. You could average the RMSD together resulting from each,
but usually people just report all three on the same graph. Unless you are
going for a longer time scale event like folding, it’s often more efficient
sampling of phrase space to run more trajectories of shorter length anyway.
Clorice
On Tue, Sep 8, 2020 at 2:46 AM Nada Afiva <nadaafiva.gmail.com> wrote:
> Dear Rodrigo,
>
> Thanks so much for your help.
>
> However I have done the same procedure with the tutorial, and the RMSD plot
>
> is not what I want as
>
> I explained in the previous email.
>
> Thank you.
>
>
>
> Best wishes,
>
> Nadaafiva
>
>
>
>
>
> Pada tanggal Sel, 8 Sep 2020 pukul 09.52 Rodrigo Galindo-Murillo <
>
> rodrigogalindo.gmail.com> menulis:
>
>
>
> > Hello!
>
> > You can follow this tutorial:
>
> >
>
> >
>
> >
> https://amberhub.chpc.utah.edu/combining-multiple-trajectory-files-into-a-single-trajectory-and-remove-water-molecules-to-save-space/
>
> >
>
> > to combine your trajectories.
>
> >
>
> > Best,
>
> > Rodrigo.
>
> >
>
> > On Mon, Sep 7, 2020 at 5:59 PM Nada Afiva <nadaafiva.gmail.com> wrote:
>
> > >
>
> > > Dear Amber,
>
> > > I run 100 ns MD and then I repeated it 2 times, so I have 3
> trajectories
>
> > > for the same system.
>
> > > Now I want to combine the 3 trajectories into one single trajectory
> and I
>
> > > will use the single combined trajectory
>
> > > to calculate the RMSD ad other analyses.
>
> > > Please let me know how to combine the 3 trajectories into one single
>
> > > trajectory.
>
> > > Thank you.
>
> > >
>
> > > Best regards,
>
> > > Nadaafiva
>
> > > _______________________________________________
>
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>
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>
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>
> >
>
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>
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>
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>
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> >
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Received on Tue Sep 08 2020 - 02:30:02 PDT
