Hi,
As Elvis said, 2D-RMSD gives hint about the number of conformers sampled
during the course of simulation.
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.
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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Received on Sat Mar 18 2017 - 07:00:03 PDT
