OpenMM: A Hardware Independent Framework for Molecular Simulations

By P. Eastman, Vijay S. Pande. 2010

215 citations recorded by the source corpus.

The wide diversity of computer architectures today requires a new approach to software development. OpenMM is an abstraction layer for molecular mechanics simulations, allowing a single program to run efficiently on a variety of hardware platforms.

Subfields: Computer Networks and Communications, Hardware and Architecture, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computer Networks and Communications

1. Torsten Schwede
2. Leonid A. Mirny
3. Scott Habershon
4. Geoffrey Fudenberg
5. Maxim Imakaev
6. Gavin E. Crooks
7. Jerome P. Nilmeier
8. John D. Chodera

In Hardware and Architecture

1. Leonid A. Mirny
2. Scott Habershon
3. Geoffrey Fudenberg
4. Maxim Imakaev
5. Gavin E. Crooks
6. Jerome P. Nilmeier
7. John D. Chodera
8. David E. Manolopoulos

In Molecular Biology

1. Torsten Schwede
2. Thomas D. Goddard
3. T. Ferrin
4. Conrad C. Huang
5. Lorenza Bordoli
6. Gabriel Studer
7. Elaine C. Meng
8. Eric F. Pettersen

Citations in the corpus

• The SWISS-MODEL Repository—new features and functionality (2016, methodology): “energy minimization is performed using the OpenMM (25) molecular mechanics library.”
• Formation of Chromosomal Domains by Loop Extrusion (2015, methodology): “Since shifting bond positions in OpenMM is impossible without a computationally expensive re-initialization procedure, for computational efficiency, we advanced LEF dynamics by four steps at a time.”
• Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation (2011, methodology): “A custom Python code making use of the GPU-accelerated OpenMM package [63, 64, 65] and the PyOpenMM Python wrapper [66] was used to conduct the simulations.”
• Chromatin organization by an interplay of loop extrusion and compartmental segregation (2017, methodology): “Simulations were performed based on OpenMM (62, 63).”
• UCSF ChimeraX: Meeting modern challenges in visualization and analysis (2018, methodology): “42 For example, the ISOLDE flexible-fitting extension mentioned in the VR section uses OpenMM.”
• Scalable molecular dynamics on CPU and GPU architectures with NAMD. (2020, background): “85 Using Lep-ton requires no knowledge of programming at all as new variables can be expressed in conventional mathematical notation.”
• Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space. (2013, methodology): “It has been implemented in several widely used MD simulation packages (123, 124), and it has been benchmarked and its potential demonstrated in numerous applications spanning a wide range of regimes.”