OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

By P. Eastman, M. Friedrichs, John D. Chodera, Randall J. Radmer, C. M. Bruns, J. Ku, Kyle A. Beauchamp, T. J. Lane, Lee‐Ping Wang, D. Shukla and 6 more. Journal of Chemical Theory and Computation, 2012

656 citations recorded by the source corpus.

OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures. It is based on a layered architecture: the lower layers function as a reusable library that can be invoked by any application, while the upper layers form a complete environment for running molecular simulations. The library API hides all hardware-specific dependencies and optimizations from the users and developers of simulation programs: they can be run without modification on any hardware on which the API has been implemented. The current implementations of OpenMM include support for graphics processing units using the OpenCL and CUDA frameworks. In addition, OpenMM was designed to be extensible, so new hardware architectures can be accommodated and new functionality (e.g., energy terms and integrators) can be easily added.

Subfields: Computer Networks and Communications, Hardware and Architecture, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/49c68d4376a01ab024735804bc2b7fa1bbcc11be

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Citations in the corpus

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands (2017, methodology): “On the other hand, the difference in non-bonded energies is due to the different values for the vacuum permittivity constants used by NAMD, OpenMM and GROMACS.”
Chromatin organization by an interplay of loop extrusion and compartmental segregation (2017, methodology): “Simulations were performed based on OpenMM (62, 63).”
Multiensemble Markov models of molecular thermodynamics and kinetics (2016, neutral): “[19]”
Computer-Aided Drug Design Methods (2017, methodology): “Commonly used MD simulation codes include CHARMM (27), AMBER (28), NAMD, (29) GROMACS (30) and OpenMM (31).”
Weighted Ensemble Simulation: Review of Methodology, Applications, and Software (2017, neutral): “To our knowledge, the first freely available, highly scalable, and interoperable WE software package was WESTPA (74), which has been widely applied to a variety of systems ranging in scale from atomistic to cellular (2–4, 21, 22, 59, 62, 63, 75, 76) and interfaced with a diversity of dynamics engine”
CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates (2019, methodology): “Currently, CHARMM-GUI is the only available tool for the valid input setup of major MD simulation programs (Lee et al. 2016) such as CHARMM (Brooks et al. 2009), NAMD (Phillips et al. 2005), GROMACS (Hess et al. 2008), AMBER (Case et al. 2005), GENESIS (Jung et al. 2015), LAMMPS (Plimpton 1995), Des”
Spherical convolutions and their application in molecular modelling (2017, methodology): “For all structures, hydrogen atoms were added using the Reduce program (Word et al., 1999), after which partial charges were assigned using the OpenMM framework (Eastman et al., 2012), using the amber99sb force field (Hornak et al., 2006).”