MolDynPlot is a Python package used to design matplotlib-based figures of Molecular Dynamics (MD) simulation data using the simple text format YAML.

Time Series:

2D Time Series:

Sequence:

NMR HSQC:

.. only:: html

    Time Series:

    .. image:: _static/p53/rmsd.png
        :scale: 35
        :align: center

    2D Time Series:

    .. image:: _static/p53/dssp.png
        :scale: 35
        :align: center

    Sequence:

    .. image:: _static/gb3/s2.png
        :scale: 35
        :align: center
    NMR HSQC:

    .. image:: _static/mocvnh3/hsqc.png
        :scale: 35
        :align: center

• Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model
• Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields

MolDynPlot supports Python 2.7, and requires the following packages:

• h5py
• ipython
• matplotlib
• pandas
• pyyaml
• scikit-learn
• scipy

Testing requires the following additional packages:

• pytest
• pytest-cov
• coveralls

Building the documentation requires the following additional packages:

• sphinx
• sphinxcontrib.argdoc (fork including modified section headings)

Change to the MolDynPlot directory and run:

python setup.py install

MolDynPlot is developed by Karl T. Debiec, a graduate student at the University of Pittsburgh advised by Professors Lillian T. Chong and Angela M. Gronenborn.

Released under a 3-clause BSD license.