OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

Autor: Peter Eastman, Jason Swails, John D Chodera, Robert T McGibbon, Yutong Zhao, Kyle A Beauchamp, Lee-Ping Wang, Andrew C Simmonett, Matthew P Harrigan, Chaya D Stern, Rafal P Wiewiora, Bernard R Brooks, Vijay S Pande

Publikováno v: PLoS Computational Biology, Vol 13, Iss 7, p e1005659 (2017)

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

Externí odkaz: https://doaj.org/article/a3c536fb0ab14c8bbc0cb33e5bac84f0

Quantum chemical benchmark databases of gold-standard dimer interaction energies

Autor: Robert T. McGibbon, Elizabeth Decolvenaere, Karthik Siva, Je-Luen Li, John L. Klepeis, Alexander G. Donchev, Andrew G. Taube, Ka-Hei Law, David E. Shaw, Kim Palmo, Brent A. Gregersen, Cory Hargus, Michael Bergdorf

Publikováno v: Scientific Data, Vol 8, Iss 1, Pp 1-9 (2021)
Scientific Data

Advances in computational chemistry create an ongoing need for larger and higher-quality datasets that characterize noncovalent molecular interactions. We present three benchmark collections of quantum mechanical data, covering approximately 3,700 di

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b5aff6fbe09227183648753cc63710e8
https://doaj.org/article/df499c8fd96d49e28bfb321073fd8e1f

Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways

Autor: Vijay S. Pande, Todd J. Martínez, Robert T. McGibbon, Lee-Ping Wang

Publikováno v: Journal of chemical theory and computation, vol 12, iss 2
Wang, LP; McGibbon, RT; Pande, VS; & Martinez, TJ. (2016). Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways. Journal of Chemical Theory and Computation, 12(2), 638-649. doi: 10.1021/acs.jctc.5b00830. UC Davis: Retrieved from: http://www.escholarship.org/uc/item/1tg8t7k1

© 2015 American Chemical Society. We describe a flexible and broadly applicable energy refinement method, "nebterpolation," for identifying and characterizing the reaction events in a molecular dynamics (MD) simulation. The new method is applicable

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::17662a3a529e410f2cf849386b1f8c18
https://doi.org/10.1021/acs.jctc.5b00830

Statistical Model Selection for Markov Models of Biomolecular Dynamics

Autor: Christian R. Schwantes, Robert T. McGibbon, Vijay S. Pande

Publikováno v: The Journal of Physical Chemistry B. 118:6475-6481

Markov state models provide a powerful framework for the analysis of biomolecular conformation dynamics in terms of their metastable states and transition rates. These models provide both a quantitative and comprehensible description of the long-time

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1da289e211aae8c3427eb78053c87a58
https://doi.org/10.1021/jp411822r

Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics

Autor: Robert T. McGibbon, Vijay S. Pande

Publikováno v: Journal of Chemical Theory and Computation. 9:2900-2906

Statistical modeling of long timescale dynamics with Markov state models (MSMs) has been shown to be an effective strategy for building quantitative and qualitative insight into protein folding processes. Existing methodologies, however, rely on geom

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bda53b1159af2db998e2c13acf361fff
https://doi.org/10.1021/ct400132h