AMBER Archive (2008)

Subject: AMBER: Average structure

From: James Thomas (james.protein_at_googlemail.com)
Date: Mon Apr 21 2008 - 05:21:26 CDT

Dear Amber Community

I would like to inquire if average structure of MD run, after 10 ns for a
protein of ~100aa is reliable as a starting point for further analysis?
I heard from a post-doc who is experienced in Amber, that average structure
is not reliable for short duration simulation.
I look forward to your comments / advices.

How to remove the overall translational & rotational motion in Amber9
trajectories?

Many thanks.

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