AMBER Archive (2006)

Subject: Re: AMBER: structure from MD

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Sep 26 2006 - 11:43:58 CDT

average structures only make sense if there was little structural
change during the MD run. You might also consider doing cluster analysis
and showing the representative structure from the largest cluster,
or perhaps from each cluster. The answer really depends a lot on
what you are trying to show in the picture and what the goal of
the simulations is.

Fenghui Fan wrote:

>Dear all,
>
>I want to get a structure from MD trajectory for
>publication. In order to do this, should we use the
>PDB file from the last rst file, or we get the average
>structure from a plateau period, or we get the
>structure by further energy minimized the average
>structure?
>
>I am looking forward to getting your reply.
>
>Best regards.
>
>Fenghui Fan
>
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