hi
i tried to attach the raw file but its heavy and needs approval and may
delay.
If this figure is not interpretable (since its only 1 ns, 1 ns
trajectories), would you pls tell me in general what could be inferred
about the two trajectories (convergence) from the shades of colors shown.
Also could i compare more than two trajectories?
thanking you for the immediate responses
On Sat, Mar 18, 2017 at 10:40 PM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
wrote:
> Thanks Dan, for correcting. I was not aware of option to use a different
> reference trajectory.
> Does rms2d with a different reference trajectory tries to find out
> similarity/dissimilarity between two ensembles of structures collected
> using two simulation?
> Can you please elaborate a bit? I am just curios about it.
>
> On Sat, Mar 18, 2017 at 5:36 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > On Sat, Mar 18, 2017 at 9:58 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
> > wrote:
> > > But, may we know how was it calculated? because 2-d rmsd has to give a
> > > symmetric matrix, because RMSD is a symmetric measure.
> > > But plot doesn't look symmetric.
> >
> > Note, the plot only has to be symmetric if calculated using a single
> > trajectory (i.e. same trajectory for reference and target). Cpptraj
> > lets you specify a different trajectory as a reference.
> >
> > -Dan
> >
> > >
> > >
> > > Shailesh Kumar Panday,
> > > Ph.D. Scholar,
> > > Shool of Computational and Integrative Sciences,
> > > JNU, New Delhi - 110067
> > > INDIA
> > >
> > > On Sat, Mar 18, 2017 at 11:11 AM, Elvis Martis <
> elvis.martis.bcp.edu.in>
> > > wrote:
> > >
> > >> Hi,
> > >> Generally a 2D-RMSD plots tells you about how many unique
> conformations
> > >> the MD has sampled. In short it roughly hints at the number of
> > clusters.
> > >>
> > >> Best Regards
> > >>
> > >>
> > >>
> > >> Elvis Martis
> > >> Ph.D. Student (Computational Chemistry)
> > >> at Bombay College of Pharmacy
> > >>
> > >>
> > >> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > >> W www.elvismartis.in
> > >> Skype. adrian_elvis12
> > >>
> > >>
> > >>
> > >>
> > >> -----Original Message-----
> > >> From: Mary Varughese [mailto:maryvj1985.gmail.com]
> > >> Sent: Saturday, March 18, 2017 3:26 PM
> > >> To: AMBER Mailing List <amber.ambermd.org>
> > >> Subject: [AMBER] 2D rms plot doubt
> > >>
> > >> Hi
> > >>
> > >> I do a 2D rmsd plot of two short trajectories to compare them
> > >> (convergence). The plot generated is attached.
> > >>
> > >> But i dont understand how could i interpret the resulting plot.
> > >>
> > >> could someone help me to understand the plot generated.
> > >>
> > >>
> > >> Thanking you
> > >>
> > >> mary
> > >> _______________________________________________
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> > >>
> > > _______________________________________________
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> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sat Mar 18 2017 - 10:30:03 PDT
