AMBER Archive (2006)

Subject: RE: AMBER: Obtaining an average structure from a trajectory

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 04 2006 - 19:07:18 CDT

Hi Alfredo,

> and I was wondering if there is any way to obtain an average
> single structure
> from the whole trajectory file.

Yes it is quite easy but you should think carefully about what and average
structure will tell you. Refer to the following tutorial
(http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/index.htm
) section 6.6 for details on how to do it.

Refer to the following tutorial:
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_eight/index.ht
m section 6.1.2 for a cautionary tale on the usefulness of average cartesian
structures and why lowest energy structures and cluster analysis are usually
much more informative.

All the best
Ross

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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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