Estimation and optimization of the exchange acceptance in Umbrella Sampling Replica Exchange molecular dynamics

被引:0
|
作者
Dashti, Danial Sabri [1 ,2 ]
Roitberg, Adrian [2 ,3 ]
机构
[1] Univ Florida, Dept Phys, Gainesville, FL 32611 USA
[2] Univ Florida, QTP, Gainesville, FL 32611 USA
[3] Univ Florida, Dept Chem, Gainesville, FL 32611 USA
关键词
D O I
暂无
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
133-COMP
引用
收藏
页数:1
相关论文
共 50 条
  • [1] Optimization of Umbrella Sampling Replica Exchange Molecular Dynamics by Replica Positioning
    Dashti, Danial Sabri
    Roitberg, Adrian E.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2013, 9 (11) : 4692 - 4699
  • [2] Implementation of replica-exchange umbrella sampling in GAMESS
    Ito, Shingo
    Fedorov, Dmitri G.
    Okamoto, Yuko
    Irle, Stephan
    [J]. COMPUTER PHYSICS COMMUNICATIONS, 2018, 228 : 152 - 162
  • [3] Optimization and convergence metrics for replica exchange molecular dynamics
    Roitberg, Adrian E.
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2007, 234
  • [4] Optimization of replica exchange molecular dynamics by fast mimicking
    Hritz, Jozef
    Oostenbrink, Chris
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2007, 127 (20):
  • [5] Exchange frequency in replica exchange molecular dynamics
    Sindhikara, Daniel
    Meng, Yilin
    Roitberg, Adrian E.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2008, 128 (02):
  • [6] Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations
    Tsukamoto, Shuichiro
    Sakae, Yoshitake
    Itoh, Yukihiro
    Suzuki, Takayoshi
    Okamoto, Yuko
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2018, 148 (12):
  • [7] Multidimensional Umbrella Sampling and Replica-Exchange Molecular Dynamics Simulations for Structure Prediction of Transmembrane Helix Dimers
    Li, Pai-Chi
    Miyashita, Naoyuki
    Im, Wonpil
    Ishido, Satoshi
    Sugita, Yuji
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2014, 35 (04) : 300 - 308
  • [8] Study of Ligand Binding Selectivity of Histone Deacetylases by Replica-Exchange Umbrella Sampling Molecular Dynamics Simulations
    Tsukamoto, Shuichiro
    Sakae, Yoshitake
    Itoh, Yukihiro
    Suzuki, Takayoshi
    Okamoto, Yuko
    [J]. BIOPHYSICAL JOURNAL, 2016, 110 (03) : 544A - 545A
  • [9] Replica Exchange Molecular Dynamics
    Peng, Cheng
    Wu, Leyun
    Xu, Zhijian
    Zhu, Weiliang
    [J]. PROGRESS IN CHEMISTRY, 2022, 34 (02) : 384 - 396
  • [10] Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules
    Oshima, Hiraku
    Re, Suyong
    Sugita, Yuji
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (10) : 5199 - 5208