Metadata-Version: 2.1
Name: gromacs-py
Version: 1.0.3
Summary: Gromacs_py is a python library allowing a simplified use of the gromacs MD simulation software.
Home-page: https://github.com/samuelmurail/gromacs_py
Author: Samuel Murail
Author-email: samuel.murail@univ-paris-diderot.fr
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/samuelmurail/gromacs_py/issues
Project-URL: Funding, https://www.impots.gouv.fr/portail/
Project-URL: Source, https://github.com/samuelmurail/gromacs_py
Description: 
        
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        Gromacs_py
        =======================================
        
        
        Gromacs_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.
        One of the main objective of the gromacs_py wrapper is to automatize routine operations for MD simulation of multiple systems.
        
        * Online Documentation:
           https://gromacs-py.readthedocs.io
        
        * Source code repository:
           https://github.com/samuelmurail/gromacs_py
        
        Main features:
        ---------------------------------------
        
        * Python Scriptable simulation:
           - Topologie creation
           - Solvation
           - Ion insertion
           - Energy minimisation
           - Equilibration with position restraints
           - Production
           - **GPU** acceleration
        
        * Topologie manipulation starting from a raw ``PDB``:
           - Amino acid protonation and pKa calculation using `apbs/pdb2pqr <http://www.poissonboltzmann.org/>`_
           - Position constraints file ``.itp`` creation
           - Cyclic petide topologie
        
        * Coordinate manipulation:
           - Changing atom names, chain, coordinates, ...
           - Insertion of *N* copy of a molecule in a system for *flooding* simulation
           - Linear peptide creation
        
        * Advanced simulation tools:
           - Monitor a simulation while running
           - Interrupt a simulation if a criterion is met
        
        
        Compatibility
        ---------------------------------------
        
        * Supported Gromacs versions:
           - 2019*
           - 2018*
           - 2017
           - 2016
           - 5.1
           - 5.0
        
        * Supported Python versions:
           - 3.7*
           - 3.6*
           - 3.5*
        
        * Supported OS:
           - osx*
           - linux*
        
        **\*** tested after each code submission.
        
        Quick install
        ---------------------------------------
        
        If gromacs (version >= 5.1) is already install, then install you need to install the `gromacs_py` library, and add the gromacs `gmx` command in the environmnent variable `$PATH`:
        
        .. code-block:: bash
        
           pip install gromacs_py
        
           # Add gromacs 'gmx' path:
           export PATH='*path_to_gromacs*/bin/':$PATH
        
        
        Tutorial
        ---------------------------------------
        
        Here is an example of a short simulation of the SH3 domain of phospholipase Cγ1.
        Seven successive steps are used:
        
        1. Topologie creation using ``create_top.py``.
        2. Minimisation of the structure using ``minimize_pdb.py``.
        3. Solvation of the system using ``solvate_ions.py``.
        4. Minimisation of the system using ``minimize_pdb.py``.
        5. Equilibration of the system using ``equi_3_step.py``.
        6. Production run using ``production.py``.
        7. Extension of the production run using ``extend.py``.
        
        .. code-block:: bash
        
           # Create topologie
           gromacs_py/create_top.py -f gromacs_py/test/input/1y0m.pdb  -o tmp/1y0m/top -vsite
        
           # Minimize the protein structure
           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
        
           # Add water and ions
           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
        
           # Minimize the system
           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
        
           # Do three small equilibrations with postion contraints on heavy atoms (first), Carbon alpha (second) and low constraint on Carbon alpha (third)
           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
        
           # Small production run of 0.1 ns
           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
        
           # Extension of the simulation
           gromacs_py/extend.py -s tmp/1y0m_water_ions/03_prod/prod_1y0m.tpr -time 0.2
        
           # Remove simulation files
           rm -r ./tmp
        
        Or simply use one command to do all previous commands:
        
        .. code-block:: bash
        
           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
        
        Authors
        ---------------------------------------
        
        * `Samuel Murail <https://samuelmurail.github.io/PersonalPage/>`_, Associate Professor - `Université Paris Diderot <https://www.univ-paris-diderot.fr>`_, `CMPLI <http://bfa.univ-paris-diderot.fr/equipe-8/>`_.
        
        See also the list of `contributors <https://github.com/samuelmurail/gromacs_py/contributors>`_ who participated in this project.
        
        License
        ---------------------------------------
        
        This project is licensed under the GNU General Public License v2.0 - see the ``LICENSE`` file for details.
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.5
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.0
Description-Content-Type: text/x-rst
