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 - 10:00:02 PDT
