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 - 03:30:03 PDT
