Understanding the applicability and limitations of Wang-Landau method for biomolecules: Met-enkephalin and Trp-cage

被引：7

作者：

Singh, Priya ^{[2
]}

Sarkar, Subir K. ^{[2
]}

Bandyopadhyay, Pradipta ^{[1
]}

机构：

[1] Jawaharlal Nehru Univ, Sch Computat & Integrat Sci, New Delhi 110067, India

[2] Jawaharlal Nehru Univ, Sch Phys Sci, New Delhi 110067, India

来源：

CHEMICAL PHYSICS LETTERS | 2011年 / 514卷 / 4-6期

关键词：

FREE-ENERGY LANDSCAPE; DENSITY-OF-STATES; MONTE-CARLO; MOLECULAR-DYNAMICS; FORCE-FIELD; SIMULATIONS; PROTEINS; ECEPP/3; ALGORITHMS; EFFICIENT;

D O I：

10.1016/j.cplett.2011.08.053

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Wang-Landau (WL) method is an efficient way to calculate density of states (DOS), thermodynamic and structural properties of a system. In this work, two different flavors of WL method, its original implementation and the t (1) method of Belardinelli et al., are applied to met-enkephalin and Trp-cage to understand their efficacy and limitations. Accurate thermodynamic and structural quantities are calculated for both the peptides considered. For Trp-cage, fragmenting the energy range into different parts and determining DOS for each part is found to be a feasible way to use WL method. The problem of low temperature sampling of WL method is discussed. (C) 2011 Elsevier B. V. All rights reserved.

引用

页码：357 / 361

页数：5

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