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https://ci.appveyor.com/api/projects/status/3sobexd0dobfha09?svg=true\n    :target: https://ci.appveyor.com/project/jaimergp/ommprotocol\n\n.. image:: https://anaconda.org/insilichem/ommprotocol/badges/downloads.svg\n    :target: https://anaconda.org/InsiliChem/ommprotocol\n\n.. image:: https://readthedocs.org/projects/ommprotocol/badge/?version=latest\n    :target: http://ommprotocol.readthedocs.io/en/latest/?badge=latest\n    :alt: Documentation Status\n\n.. image:: https://img.shields.io/badge/doi-10.26434%2Fchemrxiv.7059263-blue.svg\n    :target: https://chemrxiv.org/articles/OMMProtocol_A_Command_Line_Application_to_Launch_Molecular_Dynamics_Simulations_with_OpenMM/7059263\n\nA command line application to launch molecular dynamics simulations with OpenMM\n\n.. image:: https://raw.githubusercontent.com/insilichem/ommprotocol/master/docs/img/ommprotocol.gif\n\n\nSome cool features\n------------------\n\n+ No coding required - just a YAML input file!\n+ Smart support for different input file formats:\n    + **Topology**: PDB/PDBx, Mol2, Amber's PRMTOP, Charmm's PSF, Gromacs' TOP, Desmond's DMS\n    + **Positions**: PDB, COOR, INPCRD, CRD, GRO\n    + **Velocities**: PDB, VEL\n    + **Box vectors**: PDB, XSC, CSV, INPCRD, GRO\n    + A fallback method is implemented and will attempt to load verything else that might be supported by `ParmEd \u003chttp://parmed.github.io/ParmEd/html/index.html\u003e`_.\n+ Choose your preferred **trajectory** format (PDB, PDBx, DCD, HDF5, NETCDF, MDCRD) and **checkpoints** (Amber's, CHARMM's, OpenMM XML states).\n+ Live report of simulation progress, with estimated ETA and speed.\n+ Checkpoint every *n* steps. Also, emergency rescue files are created if an error occurs.\n+ Autochunk the trajectories for easy handling.\n\n\nInstallation \u0026 usage\n--------------------\nDownload the `latest installer \u003chttps://github.com/insilichem/ommprotocol/releases/latest\u003e`_ or use ``conda install -c omnia -c insilichem ommprotocol`` if you already have Anaconda/Miniconda installed. Further details `here \u003chttp://ommprotocol.readthedocs.io/en/latest/install.html\u003e`_.\n\nWhen installed, you should be able to run:\n\n::\n\n    ommprotocol \u003cinputfile.yaml\u003e\n\nCheck the `documentation \u003chttp://ommprotocol.readthedocs.io/en/latest/input.html\u003e`_ to read more on how to create input files for OMMProtocol.\n\n\nGet help\n--------\n\n.. image:: https://readthedocs.org/projects/ommprotocol/badge/?version=latest\n    :target: http://ommprotocol.readthedocs.io/en/latest/?badge=latest\n    :alt: Documentation Status\n\nDocumentation is always available at `ReadTheDocs \u003chttp://ommprotocol.readthedocs.io\u003e`_. If you have problems running ``ommprotocol``, feel free to `create an issue \u003chttps://github.com/insilichem/ommprotocol/issues\u003e`_! Also, make sure to visit our main webpage at `insilichem.com \u003chttp://www.insilichem.com\u003e`_.\n\n\nCitation\n--------\n\nOMMProtocol 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 and available as a pre-print in ChemRxiv.\n\n.. code-block:: latex\n\n    @article{ommprotocol,\n    author    = {Rodríguez-Guerra Pedregal, Jaime and\n                 Alonso-Cotchico, Lur and\n                 Velasco-Carneros, Lorea and\n                 Maréchal, Jean-Didier}\n    title     = {OMMProtocol: A Command Line Application to Launch Molecular Dynamics Simulations with OpenMM},\n    url       = {https://chemrxiv.org/articles/OMMProtocol_A_Command_Line_Application_to_Launch_Molecular_Dynamics_Simulations_with_OpenMM/7059263/1},\n    DOI       = {10.26434/chemrxiv.7059263.v1}\n    publisher = {ChemRxiv},\n    year      = {2018},\n    month     = {Sep}\n    }\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsilichem%2Fommprotocol","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finsilichem%2Fommprotocol","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsilichem%2Fommprotocol/lists"}