Article
Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program
Methods of Molecular Biology
(2015)
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.
Keywords
- Brownian dynamics simulation,
- UHBD program,
- Helix-capping motifs,
- Conformational distribution of peptides
Disciplines
Publication Date
January 1, 2015
DOI
10.1007/978-1-4939-2285-7_5
Citation Information
Tongye Shen and Chung F. Wong. "Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program" Methods of Molecular Biology Vol. 1268 (2015) p. 75 - 87 Available at: http://works.bepress.com/chung-wong/8/