[AMBER] 2DRMS before clustering

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Sat, 7 Mar 2020 16:46:56 +0000

Hi everyone,
I have been trying to read about clustering and its importance in analyzing diverse ensemble of conformations in MD trajectories.
While going through the mailing list I came upon the "2DRMS" people have recommended prior to doing a clustering analysis.
I went through the rms2d/2drms in cpptraj in AMBER18 manual but will be grateful if someone sheds light on what context is it important and in a plain protein in explicit water simulations, how can I use 2DRMS to get an idea of various clusters of populations in my 100ns trajectory.
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Received on Sat Mar 07 2020 - 09:00:01 PST
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