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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Received on Sat Mar 18 2017 - 10:30:03 PDT
