[AMBER] Average Conformations from trajectory

From: Covington, Cody Lance <cody.l.covington.Vanderbilt.Edu>
Date: Thu, 5 Sep 2013 13:33:39 +0000


I have some simulations of a small molecule in water and in a micellar aggregate. I was wanting to analyze the conformations present in both trajectories for comparison. I would like an output of the most common conformations with the percentage of time that the structures were occupied.

I have found in ptraj that dihedral angles can be calculated, but I really need to look at multiple internal coordinates at the same time. Could anyone help with this please?

Thank you
Cody Covington

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Received on Thu Sep 05 2013 - 07:00:02 PDT
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