Electrostatics interactions are dominant in many molecular interactions, especially those affecting diffusion of molecules within a molecular system. The program UHBD (University of Houston Brownian Dynamics) computes electrostatics in ionic solution using the Poisson-Boltzmann equation. Brownian dynamics can then be used to examine diffusional processes in systems, including rates for diffusion of ligands to active sites in enzymes or the motion of critical loops on protein surface. An optional module in QUANTA allows visualization of electrostatic maps and diffusion trajectories.
Steve Herbert
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