An Overview of String-Based Path Sampling Methods

Christina Bergonzo; Carlos Simmerling

doi:10.1016/B978-0-444-53835-2.00004-3

An Overview of String-Based Path Sampling Methods

Christina Bergonzo
, Carlos Simmerling

Laufer Center for Physical and Quantitative Biology

Stony Brook University

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

4 Scopus citations

Abstract

Calculating and optimizing the minimum energy pathway of a conformational or chemical transition is important to understanding its behavior. In this review, we summarize double-ended transition state search methods, focusing on chain-of-states methods such as nudged elastic band and string method. Optimization of the paths and application to biological and chemical problems will also be discussed.

Original language	English
Pages (from-to)	89-97
Number of pages	9
Journal	Annual Reports in Computational Chemistry
Volume	7
DOIs	https://doi.org/10.1016/B978-0-444-53835-2.00004-3
State	Published - 2011

Keywords

Chain-of-states
MEP
Nudged elastic band
String method
Transition path

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10.1016/B978-0-444-53835-2.00004-3

Cite this

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title = "An Overview of String-Based Path Sampling Methods",

abstract = "Calculating and optimizing the minimum energy pathway of a conformational or chemical transition is important to understanding its behavior. In this review, we summarize double-ended transition state search methods, focusing on chain-of-states methods such as nudged elastic band and string method. Optimization of the paths and application to biological and chemical problems will also be discussed.",

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AU - Bergonzo, Christina

AU - Simmerling, Carlos

PY - 2011

Y1 - 2011

N2 - Calculating and optimizing the minimum energy pathway of a conformational or chemical transition is important to understanding its behavior. In this review, we summarize double-ended transition state search methods, focusing on chain-of-states methods such as nudged elastic band and string method. Optimization of the paths and application to biological and chemical problems will also be discussed.

AB - Calculating and optimizing the minimum energy pathway of a conformational or chemical transition is important to understanding its behavior. In this review, we summarize double-ended transition state search methods, focusing on chain-of-states methods such as nudged elastic band and string method. Optimization of the paths and application to biological and chemical problems will also be discussed.

KW - Chain-of-states

KW - MEP

KW - Nudged elastic band

KW - String method

KW - Transition path

UR - https://www.scopus.com/pages/publications/80054018930

U2 - 10.1016/B978-0-444-53835-2.00004-3

DO - 10.1016/B978-0-444-53835-2.00004-3

M3 - Article

AN - SCOPUS:80054018930

SN - 1574-1400

VL - 7

SP - 89

EP - 97

JO - Annual Reports in Computational Chemistry

JF - Annual Reports in Computational Chemistry

ER -

An Overview of String-Based Path Sampling Methods

Abstract

Keywords

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