title: Brownian dynamics simulation of peptides with the University of Houston Brownian Dynamics (UHBD) program.
abstract: 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.
authors.affiliation: Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Tongye
authors.initials: T
authors.lastname: Shen
authors.forename: Chung F
authors.initials: CF
authors.lastname: Wong
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*
chemical_list: D010455:Peptides