Brownian dynamics


Brownian dynamics provides an attractive computational approach for simulating the permeation of ions over long time-scales without having to treat all the solvent molecules explicitly. The approach consists in integrating stochastic equation of motions with some effective potential which incorporates the systematic influence of the environment. To account for non-equilibrium boundary conditions found in ion channel systems (asymetric ion concentration and transmembrane potential) we have developed a method combining the Grand Canonical Monte Carlo algorithm with Brownian dynamics, GCMC/BD (Im et al, 2000).