Dear Clorice,
I see Nada's question, perhaps like a cluster analysis derived from 3
independent of multiple independent trajectories.
As an example in this tutorial:
https://amberhub.chpc.utah.edu/clustering-a-protein-trajectory/
*(Thanks Amber-hub, it's up again)*
Is it possible if we use the idea from this
(*
https://amberhub.chpc.utah.edu/clustering-a-protein-trajectory/
<
https://amberhub.chpc.utah.edu/clustering-a-protein-trajectory/>*) to
analyze RMSD from combining 3 independent trajectories?
Thank
Setyanto Tri Wahyudi
-------
Biophysics Division,
Department of Physics - IPB University
Gedung Fisika Wing-S Lt.2 Jl. Meranti
Kampus IPB Darmaga
Bogor - 16680
Indonesia
On Tue, Sep 8, 2020 at 4:26 PM Clorice Reinhardt <clorice.reinhardt.yale.edu>
wrote:
> 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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Received on Tue Sep 08 2020 - 03:00:02 PDT
