On Sat, Mar 18, 2017 at 1:10 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.
It's effectively like running multiple RMSD calculations in a row,
each with a different reference trajectory. The original reason I
added the functionality was to compare the same trajectory before and
after I've done something to it, like minimize all of the structures.
How asymmetric the resulting plot is can be an indication of how much
the structures changed from the minimization. Honestly it's not
something that I use very often but it wasn't hard to code up so why
not, right? :-)
-Dan
>
> 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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--
-------------------------
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
