OMMProtocol: A Command Line Application to Launch Molecular Dynamics Simulations with OpenMM

10 September 2018, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

OpenMM is a free and GPU-accelerated Molecular Dynamics (MD) engine written as a layered and reusable library. This approach allows maximum flexibility to configure MD simulations and develop new molecular mechanics (MM) methods. However, this powerful versatility comes at a cost: the user is expected to write Python scripts to run a simulation. OMMProtocol aims to fill this gap by stitching OpenMM and additional third-party modules together, providing an easy way to create an input file to configure a full multi-stage simulation protocol, from minimization to equilibration and production. OMMProtocol is LGPL-licensed and freely available at https://github.com/insilichem/ommprotocol.

Keywords

molecular dynamics
software development
Python source code
command line tool

Supplementary materials

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ommprotocol-supporting
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ommprotocol-technical-documentation
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ommprotocol-src
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Supplementary weblinks

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