RE: AMBER: the averaged structure VS the specific snapshot

From: Yong Duan <>
Date: Thu, 22 Dec 2005 22:38:00 -0800

Average structure is usually a poor representation of your ns-scale
simulations which sample, presumably, many conformations. As you noted, the
average structures usually have bad geometry. What you can compare is
between the sets of conformations sampled during the simulations. A useful
approach is to classify the structures into "clusters". You then can compare
the differences among the clusters including both the structures and the
population. I think ptraj can do clustering for you.

-----Original Message-----
From: [] On Behalf Of
haixiao jin
Sent: Thursday, December 22, 2005 8:24 PM
Subject: AMBER: the averaged structure VS the specific snapshot

dear AMBER users,
     i have got the averaged structures of 400ps to 900ps of two MD
simulations and superimposed them to compare the differnce between them. is
it reasonable to get averaged structure to make comparsion? it seems that
the averaged structure is not a real structure. or should I get the specific
structure to do comparision? i am not sure. would someone help me? thank

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Received on Wed Jan 04 2006 - 18:16:50 PST
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