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Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks.

, , , and . J. Comput. Chem., 39 (21): 1682-1689 (2018)

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Integrating Scientific Programming in Communities of Practice for Students in the Life Sciences., , and . PEARC, page 83:1-83:6. ACM, (2019)Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks., , , and . J. Comput. Chem., 39 (21): 1682-1689 (2018)Polarizable force field for RNA based on the classical drude oscillator., and . J. Comput. Chem., 39 (32): 2624-2646 (2018)Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes., and . J. Chem. Inf. Model., 63 (21): 6851-6862 (November 2023)TUPÃ: Electric field analyses for molecular simulations., and . J. Comput. Chem., 43 (16): 1113-1119 (2022)Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies., , and . Journal of Chemical Information and Modeling, 50 (12): 2221-2235 (2010)Ion Binding Properties and Dynamics of the bcl-2 G-Quadruplex Using a Polarizable Force Field., , and . J. Chem. Inf. Model., 60 (12): 6476-6488 (2020)CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field., , , , , , , , and . J. Comput. Chem., 43 (5): 359-375 (2022)Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model., , , and . J. Comput. Chem., 36 (19): 1473-1479 (2015)DIRECT-ID: An automated method to identify and quantify conformational variations - application to β2-adrenergic GPCR., , , and . J. Comput. Chem., 37 (4): 416-425 (2016)