GNM based trajectory analysis

[GoogleCodeExporter]

I've successfully used the Gaussian network model to analyse trajectories to 
pick out conformational transitions and other interesting features (Hall et al 
JACS 2007, http://dx.doi.org/10.1021/ja071797y ). To add this functionality to 
MDAnalysis I've written a small GNM analysis module (gnm.py, to go in 
analysis), and an example script using the standard test data (GNMExample.py). 
Any comments or suggestions are welcome

Original issue reported on code.google.com by hall...@gmail.com on 5 Dec 2011 at 10:21

Attachments:

• gnm.py
• GNMExample.py

[GoogleCodeExporter]

neat!

Original comment by orbeckst on 5 Dec 2011 at 4:30

• Changed state: Started
• Added labels: Type-Enhancement
• Removed labels: Type-Defect

[GoogleCodeExporter]

added to master and will be included in 0.7.5

Original comment by orbeckst on 8 Dec 2011 at 5:28

• Changed state: Fixed
• Added labels: ****
• Removed labels: ****

[GoogleCodeExporter]

Hi Ben,

I added some docs; when you get a chance check that this is ok and change as 
appropriate.

http://mdanalysis.googlecode.com/git/package/doc/html/documentation_pages/analys
is/gnm.html

(The docs are in analysis/gnm.py).

Cheers,
Oli

Original comment by orbeckst on 12 Feb 2012 at 9:28

• Added labels: ****
• Removed labels: ****