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

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.
