=========== OMMProtocol

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A command line application to launch molecular dynamics simulations with OpenMM

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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

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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 and available as a pre-print in ChemRxiv.

.. code-block:: latex

@article{ommprotocol,
author    = {Rodríguez-Guerra Pedregal, Jaime and
             Alonso-Cotchico, Lur and
             Velasco-Carneros, Lorea and
             Maréchal, Jean-Didier}
title     = {OMMProtocol: A Command Line Application to Launch Molecular Dynamics Simulations with OpenMM},
url       = {https://chemrxiv.org/articles/OMMProtocol_A_Command_Line_Application_to_Launch_Molecular_Dynamics_Simulations_with_OpenMM/7059263/1},
DOI       = {10.26434/chemrxiv.7059263.v1}
publisher = {ChemRxiv},
year      = {2018},
month     = {Sep}
}