Replica exchange Gaussian accelerated molecular dynamics: Improved enhanced sampling and free energy calculation

被引：0
|
作者：
Huang, Yu-ming [1 ]
McCammon, J. Andrew [2 ]
Miao, Yinglong [3 ,4 ]
机构：
[1] Univ Calif San Diego, Dept Chem & Biochem, San Diego, CA 92103 USA
[2] Univ Calif San Diego, La Jolla, CA 92093 USA
[3] Univ Kansas, Ctr Computat Biol, Lawrence, KS 66045 USA
[4] Univ Kansas, Dept Mol Biosci, Lawrence, KS 66045 USA
来源：
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY | 2018年 / 256卷
关键词：
D O I：
暂无
中图分类号：
O6 [化学];
学科分类号：
0703 ;
摘要：
250
引用
收藏
页数：1
相关论文
共 50 条
  • [1] Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation
    Huang, Yu-ming M.
    McCammon, J. Andrew
    Miao, Yinglong
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2018, 14 (04) : 1853 - 1864
  • [2] Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems
    Hasse, Timothy
    Huang, Yu-ming M.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2024, 20 (15) : 6485 - 6499
  • [3] Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation
    Miao, Yinglong
    Feher, Victoria A.
    McCammon, J. Andrew
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2015, 11 (08) : 3584 - 3595
  • [4] 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
  • [5] Gaussian accelerated molecular dynamics: Unconstrained enhanced sampling and free energy calculation of biomolecules
    Miao, Yinglong
    McCammon, J. Andrew
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2016, 251
  • [6] Accelerating Solvent Dynamics with Replica Exchange for Improved Free Energy Sampling
    Darkins, Robert
    Duffy, Dorothy M.
    Ford, Ian J.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2023, 19 (21) : 7527 - 7532
  • [7] Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods
    Roe, Daniel R.
    Bergonzo, Christina
    Cheatham, Thomas E., III
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2014, 118 (13): : 3543 - 3552
  • [8] Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
    Miao, Yinglong
    Sinko, William
    Pierce, Levi
    Bucher, Denis
    Walker, Ross C.
    McCammon, J. Andrew
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2014, 10 (07) : 2677 - 2689
  • [9] Using Multistate Free Energy Techniques to Improve the Efficiency of Replica Exchange Accelerated Molecular Dynamics
    Fajer, Mikolai
    Swift, Robert V.
    McCammon, J. Andrew
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (11) : 1719 - 1725
  • [10] Fast and Accurate Calculation of Small Molecule Solvation Free Energies using Replica Exchange Accelerated Molecular Dynamics
    Arrar, Mehrnoosh
    Sinko, William
    Fajer, Mikolai
    Agusto, Cesar
    de Oliveira, F.
    McCammon, J. Andrew
    [J]. BIOPHYSICAL JOURNAL, 2012, 102 (03) : 447A - 447A
12345