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
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
收藏
页码:357 / 361
页数:5
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