[AMBER] representing structure from equilibrium

From: newamber list <newamberlist.gmail.com>
Date: Mon, 4 May 2015 17:35:25 +0100

Hi All

I want to use some representing structure from equilibrated part of
trajectory. One way is to use an Average structure but being an 'average'
it can not be directly used for simulations as it can have unusual bonding
(length, angles) information.

Another way someone suggested me is Clustering analysis. As far as I
googled this term, one gets few clusters and one can choose lowest RMSD
structure from centroid of most populated cluster. I am just wondering
would this be a good way of choosing best representing structure?

Also cpptraj manual suggests there are two algorithms to choose. Which one
I should use in my case. Also, when someone says 'distance from centroid'
does it usually means RMSD? I am confused with terminologies used.

Thanks for any help.
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Received on Mon May 04 2015 - 10:00:04 PDT
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