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======================= 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.