{
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        "author": "Samuel Murail",
        "author_email": "samuel.murail@univ-paris-diderot.fr",
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        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
            "Natural Language :: English",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": ".. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1455734.svg\n   :target: https://doi.org/10.5281/zenodo.1455734\n\n\n.. image:: https://readthedocs.org/projects/gromacs-py/badge/?version=latest\n   :target: https://gromacs-py.readthedocs.io/en/latest/?badge=latest\n   :alt: Documentation Status\n\n\n.. image:: https://travis-ci.org/samuelmurail/gromacs_py.svg?branch=master\n    :target: https://travis-ci.org/samuelmurail/gromacs_py\n\n.. image:: https://codecov.io/gh/samuelmurail/gromacs_py/branch/master/graph/badge.svg\n  :target: https://codecov.io/gh/samuelmurail/gromacs_py\n\n.. image:: https://anaconda.org/samuel.murail/gromacs_py/badges/version.svg\n  :target: https://anaconda.org/samuel.murail/gromacs_py\n\nGromacs_py\n=======================================\n\n\nGromacs_py is a python library allowing a simplified use of the gromacs MD simulation software. Gromacs_py can build topologie based on a pdb file, create the simulation system (box, add water and ions) and run minimisation, equilibration and production run.\nOne of the main objective of the gromacs_py wrapper is to automatize routine operations for MD simulation of multiple systems.\n\n* Online Documentation:\n   https://gromacs-py.readthedocs.io\n\n* Source code repository:\n   https://github.com/samuelmurail/gromacs_py\n\nMain features:\n---------------------------------------\n\n* Python Scriptable simulation:\n   - Topologie creation\n   - Solvation\n   - Ion insertion\n   - Energy minimisation\n   - Equilibration with position restraints\n   - Production\n   - **GPU** acceleration\n\n* Topologie manipulation starting from a raw ``PDB``:\n   - Amino acid protonation and pKa calculation using `apbs/pdb2pqr <http://www.poissonboltzmann.org/>`_\n   - Position constraints file ``.itp`` creation\n   - Cyclic petide topologie\n\n* Coordinate manipulation:\n   - Changing atom names, chain, coordinates, ...\n   - Insertion of *N* copy of a molecule in a system for *flooding* simulation\n   - Linear peptide creation\n\n* Advanced simulation tools:\n   - Monitor a simulation while running\n   - Interrupt a simulation if a criterion is met\n\n\nCompatibility\n---------------------------------------\n\n* Supported Gromacs versions:\n   - 2019*\n   - 2018*\n   - 2017\n   - 2016\n   - 5.1\n   - 5.0\n\n* Supported Python versions:\n   - 3.7*\n   - 3.6*\n   - 3.5*\n\n* Supported OS:\n   - osx*\n   - linux*\n\n**\\*** tested after each code submission.\n\nQuick install\n---------------------------------------\n\nAdd several conda channels for dependencies:\n\n.. code-block:: bash\n\n   conda config --add channels conda-forge\n   conda config --add channels bioconda\n   conda config --add channels samuel.murail\n\nThen install `gromacs_py`:\n\n.. code-block:: bash\n\n   conda install gromacs_py\n\nsee `Installation <https://gromacs-py.readthedocs.io/en/latest/install.html>`_ for details.\n\n.. _github: https://github.com/samuelmurail/gromacs_py\n\nTutorial\n---------------------------------------\n\nHere is an example of a short simulation of the SH3 domain of phospholipase C\u03b31.\nSeven successive steps are used:\n\n1. Topologie creation using ``create_top.py``.\n2. Minimisation of the structure using ``minimize_pdb.py``.\n3. Solvation of the system using ``solvate_ions.py``.\n4. Minimisation of the system using ``minimize_pdb.py``.\n5. Equilibration of the system using ``equi_3_step.py``.\n6. Production run using ``production.py``.\n7. Extension of the production run using ``extend.py``.\n\n.. code-block:: bash\n\n   # Create topologie\n   gromacs_py/create_top.py -f gromacs_py/test/input/1y0m.pdb  -o tmp/1y0m/top -vsite\n\n   # Minimize the protein structure\n   gromacs_py/minimize_pdb.py -f tmp/1y0m/top/1y0m_pdb2gmx_box.pdb -p tmp/1y0m/top/1y0m_pdb2gmx.top -o tmp/1y0m/em/  -n em_1y0m -nt 2\n\n   # Add water and ions\n   gromacs_py/solvate_ions.py -f tmp/1y0m/em/em_1y0m_compact.pdb -p tmp/1y0m/top/1y0m_pdb2gmx.top -o tmp/1y0m_water_ions/top/  -n 1y0m_water_ions\n\n   # Minimize the system\n   gromacs_py/minimize_pdb.py -f tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.gro -p tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o tmp/1y0m_water_ions/em/  -n em_1y0m\n\n   # Do three small equilibrations with postion contraints on heavy atoms (first), Carbon alpha (second) and low constraint on Carbon alpha (third)\n   gromacs_py/equi_3_step.py -f tmp/1y0m_water_ions/em/em_1y0m_compact.pdb -p tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o tmp/1y0m_water_ions/  -n 1y0m -HA_time 0.1 -CA_time 0.1 -CA_LOW_time 0.1\n\n   # Small production run of 0.1 ns\n   gromacs_py/production.py -f tmp/1y0m_water_ions/02_equi_CA_LOW/equi_CA_LOW_1y0m.gro -p tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o tmp/1y0m_water_ions/03_prod -n 1y0m -time 0.1\n\n   # Extension of the simulation\n   gromacs_py/extend.py -s tmp/1y0m_water_ions/03_prod/prod_1y0m.tpr -time 0.2\n\n   # Remove simulation files\n   rm -r ./tmp\n\nOr simply use one command to do all previous commands:\n\n.. code-block:: bash\n\n   gromacs_py/top_em_equi_3_step_prod.py -f gromacs_py/test/input/1y0m.pdb -o tmp/1y0m -vsite -HA_time 0.1 -CA_time 0.1 -CA_LOW_time 0.1 -prod_time 0.3\n\nAuthors\n---------------------------------------\n\n* **Samuel Murail**, Maitre de conf\u00e9rence - `Universit\u00e9 Paris Diderot <https://www.univ-paris-diderot.fr>`_, `CMPLI <http://bfa.univ-paris-diderot.fr/equipe-8/>`_.\n\nSee also the list of `contributors <https://github.com/samuelmurail/gromacs_py/contributors>`_ who participated in this project.\n\nLicense\n---------------------------------------\n\nThis project is licensed under the GNU General Public License v2.0 - see the ``LICENSE`` file for details.",
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