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RCBS.py Examples

Repository containing Jupyter Notebooks (and eventually Python scripts) exemplifying how to use RCBS.py and what it is capable of. Example file to illustrate the code are also included.

md_analyser

Folder for storing the examples related to the md_analyser submodule.

It contains the following notebooks and example files:

  • trajectory_analysis_and_frame_extraction.ipynb: Notebook illustrating all the measurements that can be done with the submodule on a real example, as well as the application of criteria to the measurements and the extraction of the frames that satisfy the criteria.
  • parameters.prmtop: parameters in the AMBER format for the DHA/human12LOX Michaelis complex.
  • trajectory.nc: trajectory file in the NetCDF format containing 10 frames of the production stage of a MD of the DHA/human12LOX Michaelis complex.