Brownian dynamics simulation of peptides with the University of Houston Brownian Dynamics (UHBD) program

This chapter provides the background theory and a practical protocol for performing Brownian dynamics simulation of peptides. Brownian dynamics simulation represents a complementary approach to Monte Carlo and molecular dynamics methods. Unlike Monte Carlo methods, it could provide dynamical information in a timescale longer than the momentum relaxation time. On the other hand, it is faster than molecular dynamics by approximating the solvent by a continuum and by operating in the over-damped limit. This chapter introduces the use of the University of Houston Brownian Dynamics (UHBD) program [1, 2] to perform Brownian dynamics simulation on peptides.