Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program

Tongye Shen; Chung F. Wong

doi:10.1007/978-1-4939-2285-7_5

Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program

Tongye Shen, Chung F. Wong

University of Missouri-St. Louis

Research output: Contribution to journal › Article › peer-review

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.

Original language	American English
Journal	Methods of Molecular Biology
Volume	1268
DOIs	https://doi.org/10.1007/978-1-4939-2285-7_5
State	Published - Jan 1 2015

Keywords

Brownian dynamics simulation
Conformational distribution of peptides
Helix-capping motifs
UHBD program

Disciplines

Statistical, Nonlinear, and Soft Matter Physics
Physics

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10.1007/978-1-4939-2285-7_5License: Unspecified

Cite this

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AB - 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.

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KW - Conformational distribution of peptides

KW - Helix-capping motifs

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Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program

Abstract

Keywords

Disciplines

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