OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics

Autor: Andrew C. Simmonett, Bernard R. Brooks, Jason M. Swails, Rafal P. Wiewiora, Robert T. McGibbon, Peter Eastman, John D. Chodera, Kyle A. Beauchamp, Vijay S. Pande, Lee-Ping Wang, Chaya D. Stern, Yutong Zhao, Matthew P. Harrigan
Přispěvatelé: Gentleman, Robert
Rok vydání: 2016
Předmět:
0301 basic medicine
Source code
Statistical methods
Computer science
Molecular Dynamics
Extensibility
Biochemistry
01 natural sciences
Mathematical Sciences
Molecular dynamics
Software
Computational Chemistry
Biochemical Simulations
Amoebas
lcsh:QH301-705.5
media_common
Protozoans
Ecology
010304 chemical physics
Simulation and Modeling
Applied Mathematics
Software Engineering
Biological Sciences
Monte Carlo method
Chemistry
Computational Theory and Mathematics
Modeling and Simulation
Physical Sciences
Engineering and Technology
Algorithm
Simulation methods
Algorithms
Research Article
Biotechnology
Computer and Information Sciences
Bioinformatics
media_common.quotation_subject
Statistics (mathematics)
Bioengineering
Molecular Dynamics Simulation
Research and Analysis Methods
010402 general chemistry
03 medical and health sciences
Cellular and Molecular Neuroscience
Information and Computing Sciences
0103 physical sciences
Genetics
Molecular Biology
Ecology
Evolution
Behavior and Systematics

business.industry
Organisms
Biology and Life Sciences
Computational Biology
Source Code
0104 chemical sciences
030104 developmental biology
lcsh:Biology (General)
Integrator
Mathematical and statistical techniques
Programming Languages
business
Mathematics
Coding (social sciences)
Zdroj: PLoS Computational Biology, Vol 13, Iss 7, p e1005659 (2017)
PLoS computational biology, vol 13, iss 7
PLoS Computational Biology
Popis: OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.
Databáze: OpenAIRE