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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>> > >>
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>> > > AMBER.ambermd.org
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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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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
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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 - 05:30:05 PDT
