Switch branches/tags
Nothing to show
Find file History
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
..
Failed to load latest commit information.
contacts
data
example_cap_peptide
figures
output
GNMExample.py
README.txt Moved examples from main repo to Cookbook repo Jan 18, 2016
amber2dcd.py
backbone_dihedral.py
blocks.py
dcd2xtc.py
lipid_order_parameters.py Moved examples from main repo to Cookbook repo Jan 18, 2016
make_MthK_tetramer.py
membrane-composition.py
membrane-leaflets.py Moved examples from main repo to Cookbook repo Jan 18, 2016
membrane-parameters.py
multimers-analysis.py
nativecontacts.py
potential_profile.py
radial_distribution_function.py
rmsd.py
rmsd_groups.py
rmsfit.py Moved examples from main repo to Cookbook repo Jan 18, 2016
rmsfit_qcp.py
rotational_autocorrelation.py
schlitter_determ.py
schlitter_quasiharmonic.py

README.txt

=======================
Examples for MDAnalysis
=======================

These python scripts show how MDAnalysis has been used to analyze MD
trajectories produced by LAMMPS or CHARMM. They are provided as
real-world examples but no effort has been made to make them
userfriendly; in fact, they will probably not work right away for you
as many assumptions have been simply hard coded.

Many of those scripts originated with older versions of MDAnalysis and
might be broken. Feedback is appreciated as are your own example
scripts.

Please discuss these scripts on the mailing list
http://groups.google.com/group/mdnalysis-discussion or file bugs
through the issue tracker
http://issues.mdanalysis.org


.. Note:: If you try to run example scripts from the top level
   directory (such as ``python ./examples/nativecontacts.py``) then
   you will likely get an error such as *ImportError: No module named
   _dcdmodule*. The problem is that python is trying to pick up
   MDAnalysis from the *source* directory (``./MDAnalysis``) but the
   compiled libraries were installed elsewhere. The solution is to not
   be in the source directory: simply ``cd examples/`` or copy the
   examples elsewhere into your work space.


Descriptions
============

For the time being, please see the scripts for details. They are all
fairly short.