University of Houston Brownian Dynamics (UHBD)


If you use UHBD for electrostatic calculations, you might also be interested in APBS.

Electrostatics and Brownian/Molecular Dynamics Program

The UHBD (University of Houston Brownian Dynamics) program is capable of solving the linearized and non-linear Poisson-Boltzmann equation using a finite-difference method. In addition, the program can be used to perform Brownian dynamics calculations for steady and non-steady state rate constants of encounter of a substrate/inhibitor with a target (enzyme). The UHBD code can also be used to perform stochastic dynamics calculations or molecular mechanics energy minimizations using the Poisson-Boltzmann and/or other molecular mechanics forces. The program also has the capability to compute electrostatic free energies of binding of two molecules and can include the non-electrostatic surface area changes and how that affects the energy. Many other more minor methods/capabilities are available. Take a look at the manual for more details or send e-mail to Jim Briggs with questions or to find out how to obtain the code.

Click on this link for a PostScript copy of the UHBD manual. Note that this is a bit large (ca. 300 pages - 1MB).


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