Electrostatics and diffusion of molecules in solution – simulations with the University-of-Houston Brownian dynamics program. This paper is a follow-up to the initial communication (Comput. Phys. Commun. 62 (1991) 187–197) on the Brownian Dynamics/Electrostatics program UHBD developed at the University of Houston. The program is now capable of computing pKas of ionizable groups in proteins, performing Brownian dynamics simulations with a flexible substrate and target, and molecular mechanics/dynamics calculations using a continuum solvent. These new capabilities and other features are discussed along with selected applications which illustrate the capabilities of the current version of UHBD.
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References in zbMATH (referenced in 5 articles )
Showing results 1 to 5 of 5.
- Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil: Progress in developing Poisson-Boltzmann equation solvers (2013)
- Helgadóttir, Ásdís; Gibou, Frédéric: A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid (2011)
- Huber, Gary A.; McCammon, J.Andrew: Browndye: A software package for Brownian dynamics (2010)
- Lu, B.Z.; Zhou, Y.C.; Holst, M.J.; McCammon, J.A.: Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications (2008)
- Helms, Volkhard; McCammon, J.Andrew: Conformational transitions of proteins from atomistic simulations (1999)