https://github.com/insilichem/ommprotocol

A command line application to launch molecular dynamics simulations with OpenMM
https://github.com/insilichem/ommprotocol

amber command-line molecular-dynamics openmm

Last synced: 2 months ago
JSON representation

A command line application to launch molecular dynamics simulations with OpenMM

• Host: GitHub
• URL: https://github.com/insilichem/ommprotocol
• Owner: insilichem
• License: lgpl-3.0
• Created: 2016-01-26T13:45:02.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2022-04-07T12:54:00.000Z (almost 3 years ago)
• Last Synced: 2024-10-13T22:48:21.471Z (3 months ago)
• Topics: amber, command-line, molecular-dynamics, openmm
• Language: Python
• Homepage: http://ommprotocol.readthedocs.io
• Size: 1.42 MB
• Stars: 39
• Watchers: 3
• Forks: 8
• Open Issues: 9
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
===========

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

.. image:: https://img.shields.io/badge/doi-10.26434%2Fchemrxiv.7059263-blue.svg

    :target: https://chemrxiv.org/articles/OMMProtocol_A_Command_Line_Application_to_Launch_Molecular_Dynamics_Simulations_with_OpenMM/7059263

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 `_.

+ 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 `_ or use ``conda install -c omnia -c insilichem ommprotocol`` if you already have Anaconda/Miniconda installed. Further details `here `_.

When installed, you should be able to run:

::

    ommprotocol 

Check the `documentation `_ 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 `_. If you have problems running ``ommprotocol``, feel free to `create an issue `_! Also, make sure to visit our main webpage at `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}

    }