Thanks Dan,
As you pointed out comparing RMSD before and after minimization for a set
of structures, It is good use case of this functionality.
-Shailesh
On Mon, Mar 20, 2017 at 1:27 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> The plots themselves just show RMSD of structures in all trajectory
> frames to each other - low values indicate similar structure, high
> values indicate dissimilar. Hopefully this helps, but I'm still not
> really sure what you're asking. Instead of sending the raw data you're
> probably better off just describing what simulations you have
> performed and what kind of analysis you are trying to do (what you're
> hoping to see, input you gave to cpptraj, etc).
>
> -Dan
>
> On Sat, Mar 18, 2017 at 1:14 PM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> > 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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> >> >
> >> >
> >> > --
> >> > -------------------------
> >> > 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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> >> >
> >> _______________________________________________
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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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Received on Mon Mar 20 2017 - 10:00:02 PDT
