Re: [AMBER] 2DRMS before clustering

From: Rodrigo Galindo-Murillo <>
Date: Sat, 7 Mar 2020 14:10:01 -0700

Hello Debarati.

Perhaps this example will help you with the analysis.


On Sat, Mar 7, 2020 at 9:47 AM Debarati DasGupta
<> wrote:
> 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.
> Thanks
> Debarati
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Received on Sat Mar 07 2020 - 13:30:02 PST
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