Efficient simulation protocol for determining the density of states: Combination of replica-exchange Wang-Landau method and multicanonical replica-exchange method

被引:6
|
作者
Hayashi, Takuya [1 ]
Okamoto, Yuko [1 ,2 ,3 ,4 ,5 ]
机构
[1] Nagoya Univ, Grad Sch Sci, Dept Phys, Nagoya, Aichi 4648602, Japan
[2] Nagoya Univ, Struct Biol Res Ctr, Grad Sch Sci, Nagoya, Aichi 4648602, Japan
[3] Nagoya Univ, Ctr Computat Sci, Grad Sch Engn, Nagoya, Aichi 4648603, Japan
[4] Nagoya Univ, Informat Technol Ctr, Nagoya, Aichi 4648601, Japan
[5] JST CREST, Nagoya, Aichi 4648602, Japan
关键词
MONTE-CARLO SIMULATIONS; TEMPERATURE MOLECULAR-DYNAMICS; FREE-ENERGY; ENSEMBLE; ALGORITHM; PEPTIDES; ENTROPY; SYSTEMS; ICE;
D O I
10.1103/PhysRevE.100.043304
中图分类号
O35 [流体力学]; O53 [等离子体物理学];
学科分类号
070204 ; 080103 ; 080704 ;
摘要
By combining two generalized-ensemble algorithms, the replica-exchange Wang-Landau (REWL) method and the multicanonical replica-exchange method (MUCAREM), we propose an effective simulation protocol to determine the density of states with high accuracy. The new protocol is referred to as REWL-MUCAREM, and REWL is first performed and then MUCAREM is performed. In order to verify the effectiveness of our protocol, we performed simulations of a square-lattice Ising model using the three methods, namely REWL, MUCAREM, and REWL-MUCAREM. The results showed that the density of states obtained by REWL-MUCAREM is more accurate than that is estimated by the two methods separately.
引用
收藏
页数:8
相关论文
共 50 条
  • [1] Calculation of the residual entropy of Ice Ih by Monte Carlo simulation with the combination of the replica-exchange Wang-Landau algorithm and multicanonical replica-exchange method
    Hayashi, Takuya
    Muguruma, Chizuru
    Okamoto, Yuko
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2021, 154 (04):
  • [2] Scalable replica-exchange framework for Wang-Landau sampling
    Vogel, Thomas
    Li, Ying Wai
    Wuest, Thomas
    Landau, David P.
    [J]. PHYSICAL REVIEW E, 2014, 90 (02):
  • [3] A practical guide to replica-exchange Wang-Landau simulations
    Vogel, Thomas
    Li, Ying Wai
    Landau, David P.
    [J]. IX BRAZILIAN MEETING ON SIMULATIONAL PHYSICS (BMSP 2017), 2018, 1012
  • [4] Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
    Sugita, Y
    Okamoto, Y
    [J]. CHEMICAL PHYSICS LETTERS, 2000, 329 (3-4) : 261 - 270
  • [5] Implementation of the replica-exchange Wang-Landau sampling on Graphics Processing Units (GPUs)
    Boer, A.
    [J]. COMPUTER PHYSICS COMMUNICATIONS, 2018, 233 : 62 - 66
  • [6] Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test
    Mitsutake, A
    Sugita, Y
    Okamoto, Y
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2003, 118 (14): : 6664 - 6675
  • [7] Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space
    Valentim, Alexandra
    Rocha, Julio C. S.
    Tsai, Shan-Ho
    Lis, Ying Wai
    Eisenbach, Markus
    Fiore, Carlos E.
    Landau, David P.
    [J]. XXVI IUPAP CONFERENCE ON COMPUTATIONAL PHYSICS (CCP2014), 2015, 640
  • [8] The role of chain-stiffness in lattice protein models: A replica-exchange Wang-Landau study
    Farris, Alfred C. K.
    Shi, Guangjie
    Wust, Thomas
    Landau, David P.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2018, 149 (12):
  • [9] Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system
    Mitsutake, A
    Sugita, Y
    Okamoto, Y
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2003, 118 (14): : 6676 - 6688
  • [10] Fragment replica-exchange method for efficient protein conformation sampling
    Suzuki, M.
    Okuda, H.
    [J]. MOLECULAR SIMULATION, 2008, 34 (03) : 267 - 275