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The python free energy analysis toolkit

Project description

The python free energy analysis toolkit.

Please note that this code is still under heavy development!

Authors

*) equal contribution

Manifest

  • README.rst (this file)
  • LICENCE.rst
  • setup.py
  • pyfeat/ (package)
  • ext/ (C/Cython implementation)
  • iPythonNotebooks/ (examples)

Getting started

For a development installation from source, run

python setup.py develop --user --verbose

and make sure, that your PATH and PYTHONPATH environment variables are set and include the bin and site-packages directories which you can find in the verbose output.

For a regular installation, run

python setup.py install [--user] [--verbose]

Example: MBAR (via shell script)

Go to your bash and run

cd PATH_TO_REPOSITORY/iPythonNotebooks
python generators/gen_st_adwp.py
run_mbar.py --verbose data/ST_ADW/replica.dat --kT_file data/ST_ADW/kT.dat

Example: WHAM (via shell script)

Go to your bash and run

cd PATH_TO_REPOSITORY/iPythonNotebooks
python generators/gen_st_adwp.py
run_wham.py --verbose data/ST_ADW/replica.dat --kT_file data/ST_ADW/kT.dat --wham_file data/ST_ADW/st_wham.dat

References

  • Shirts MR and Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. J. Chem. Phys. 129:124105 (2008).
  • Kumar, S. et al. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comp. Chem. 13(8), 1011–1021 (1992).

Project details


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