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README.md

ZIBMolPy

ZIBMolPy

What's this?

The core of the ZIBMolPy package is an implementation of the efficient, adaptive sampling algorithm ZIBgridfree, designed for characterizing the conformational space of molecules.

The original ZIBgridfree algorithm was designed by Marcus Weber and Holger Meyer in 2005, and, over the years, has been enhanced by Alexander Riemer, Susanna Röblitz and Lionel Walter. The theoretical framework of ZIBgridfree is provided by Conformation Dynamics, an idea coined by Peter Deuflhard and Christoph Schütte.

This implementation represents an evolution of the original ZIBgridfree as it couples the original algorithm to the state-of-the-art molecular dynamics engine Gromacs. This creates the possibility to apply ZIBgridfree to very large molecular systems.

ZIBMolPy is currently being developed by Alexander Bujotzek, Ole Schütt and Adam Nielsen in the working group of Marcus Weber at Zuse-Institute Berlin. A manuscript for publication is in preparation:

  • A. Bujotzek, O. Schütt, K. Fackeldey, M. Weber: ZIBgridfree: Efficient conformational analysis by meshless uncoupling-coupling

License

This software package is released under the LGPL 3.0, see LICENSE file.

Screenshots

ZIBgridfree Browser

ZIBgridfree Browser, the graphical user interface of ZIBgridfree.

ZIBgridfree Browser

Monitor the distribution of your internal coordinates as it is sampled.

ZIBgridfree Browser

Analyze thermodynamics and identify metastable conformations.

Installation

Prerequisites

You have to install a bunch of packages. On Ubuntu/Debian you can simply type:

sudo apt-get install python-numpy python-scipy python-matplotlib python-gtk2 gromacs

Download

  1. Download the current 'master' version as zipball or tarball.

  2. Extract it with e.g.
    tar -xvzf CMD-at-ZIB-ZIBMolPy-80c927a.tar.gz

  3. Go into the the directory:
    cd CMD-at-ZIB-ZIBMolPy-xxxxxx

Alternatively, use git to obtain the code:
git clone git://github.com/CMD-at-ZIB/ZIBMolPy.git (read-only)
git clone git@github.com:CMD-at-ZIB/ZIBMolPy.git (read+write)

System-wide installation

Run:
sudo make install

Installation into home directory

  1. Run
    make install-home

  2. Add the following lines to your .bashrc:
    export PYTHONPATH=$PYTHONPATH:~/lib/pythonX.X/site-packages/
    export PATH=$PATH:~/bin/

Installation into custom location

  1. Run
    make prefix=~/my_favorite_location install

  2. Add the following lines to your .bashrc:
    export PYTHONPATH=$PYTHONPATH:~/my_favorite_location/lib/pythonX.X/site-packages/
    export PATH=$PATH:~/my_favorite_location/bin/

Testing

You can run some tests to make sure everything is working as intended.

  1. Go into the tests/ directory, which is located either in
    /usr/share/zibmolpy/tests or
    ~/usr/share/zibmolpy/tests, or according to your own prefix.

  2. Choose one of the tests cases. The pentane_quick test takes the least amount of time to run.

  3. Depending on your Gromacs version run either
    zgf_test test-desc-seq-gromacs-4.0.7.xml
    or
    zgf_test test-desc-seq-gromacs-4.5.5.xml

  4. You can take a look at the results by using zgf_browser.

If tests fail due to differences in numerical values, you may be using a different version of Gromacs.

Documentation

For documentation, please refer to the wiki at:

github.com/CMD-at-ZIB/ZIBMolPy/wiki

The API documentation can be found here:

cmd-at-zib.github.com/ZIBMolPy/apidocs/