Metadata-Version: 1.1
Name: ommprotocol
Version: 0.1.11
Summary: Easy to deploy MD protocols for OpenMM
Home-page: https://github.com/insilichem/ommprotocol
Author: Jaime Rodríguez-Guerra
Author-email: jaime.rogue@gmail.com
License: LGPL
Download-URL: https://github.com/insilichem/ommprotocol/tarball/v0.1.11
Description: ===========
        OMMProtocol
        ===========
        
        .. image:: https://travis-ci.org/insilichem/ommprotocol.svg?branch=master
            :target: https://travis-ci.org/insilichem/ommprotocol
        
        .. image:: https://ci.appveyor.com/api/projects/status/3sobexd0dobfha09?svg=true
            :target: https://ci.appveyor.com/project/jaimergp/ommprotocol
        
        .. image:: https://anaconda.org/insilichem/ommprotocol/badges/downloads.svg
            :target: https://anaconda.org/InsiliChem/ommprotocol
        
        .. image:: https://readthedocs.org/projects/ommprotocol/badge/?version=latest
            :target: http://ommprotocol.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        
        A command line application to launch molecular dynamics simulations with OpenMM
        
        .. image:: https://raw.githubusercontent.com/insilichem/ommprotocol/master/docs/img/ommprotocol.gif
        
        
        Some cool features
        ------------------
        
        + No coding required - just a YAML input file!
        + Smart support for different input file formats:
            + **Topology**: PDB/PDBx, Mol2, Amber's PRMTOP, Charmm's PSF, Gromacs' TOP, Desmond's DMS
            + **Positions**: PDB, COOR, INPCRD, CRD, GRO
            + **Velocities**: PDB, VEL
            + **Box vectors**: PDB, XSC, CSV, INPCRD, GRO
            + A fallback method is implemented and will attempt to load verything else that might be supported by `ParmEd <http://parmed.github.io/ParmEd/html/index.html>`_.
        + Choose your preferred **trajectory** format (PDB, PDBx, DCD, HDF5, NETCDF, MDCRD) and **checkpoints** (Amber's, CHARMM's, OpenMM XML states).
        + Live report of simulation progress, with estimated ETA and speed.
        + Checkpoint every *n* steps. Also, emergency rescue files are created if an error occurs.
        + Autochunk the trajectories for easy handling.
        
        
        Installation & usage
        --------------------
        Download the `latest installer <https://github.com/insilichem/ommprotocol/releases/latest>`_ or use ``conda install -c omnia -c insilichem ommprotocol`` if you already have Anaconda/Miniconda installed. Further details `here <http://ommprotocol.readthedocs.io/en/latest/install.html>`_.
        
        When installed, you should be able to run:
        
        ::
        
            ommprotocol <inputfile.yaml>
        
        Check the `documentation <http://ommprotocol.readthedocs.io/en/latest/input.html>`_ to read more on how to create input files for OMMProtocol.
        
        
        Get help
        --------
        
        .. image:: https://readthedocs.org/projects/ommprotocol/badge/?version=latest
            :target: http://ommprotocol.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        Documentation is always available at `ReadTheDocs <http://ommprotocol.readthedocs.io>`_. If you have problems running ``ommprotocol``, feel free to `create an issue <https://github.com/insilichem/ommprotocol/issues>`_! Also, make sure to visit our main webpage at `insilichem.com <http://www.insilichem.com>`_.
        
        
        Citation
        --------
        
        OMMProtocol is scientific software, funded by public research grants (Spanish MINECO's project ``CTQ2014-54071-P``, Generalitat de Catalunya's project ``2014SGR989`` and research grant ``2015FI_B00768``, COST Action ``CM1306``). If you make use of Ommprotocol in scientific publications, please cite it. It will help measure the impact of our research and future funding! A manuscript is in progress. In the meantime, please cite this repository URL.
        
        .. code-block:: latex
        
            @misc{ommprotocol,
            author       = {Jaime Rodríguez-Guerra Pedregal and
                            Lur Alonso-Cotchico and
                            Lorea Velasco and
                            Jean-Didier Maréchal},
            title        = {OMMProtocol: A command line application to launch molecular dynamics simulations with OpenMM},
            url          = {https://github.com/insilichem/ommprotocol}
            }
        
Platform: any
Classifier: Programming Language :: Python
Classifier: Development Status :: 3 - Alpha
Classifier: Natural Language :: English
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Chemistry
