Fast and Accurate Calculation of Small Molecule Solvation Free Energies using Replica Exchange Accelerated Molecular Dynamics

被引:0
|
作者
Arrar, Mehrnoosh [1 ]
Sinko, William [1 ]
Fajer, Mikolai [1 ]
Agusto, Cesar [1 ]
de Oliveira, F. [1 ]
McCammon, J. Andrew [1 ]
机构
[1] Univ Calif San Diego, San Diego, CA USA
关键词
D O I
10.1016/j.bpj.2011.11.2450
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
引用
收藏
页码:447A / 447A
页数:1
相关论文
共 50 条
  • [1] Efficient and accurate calculation of proline cis/trans isomerization free energies from Hamiltonian replica exchange molecular dynamics simulations
    Kienlein, Maximilian
    Zacharias, Martin
    Reif, Maria M.
    STRUCTURE, 2023, 31 (11) : 1473 - +
  • [2] Replica exchange Gaussian accelerated molecular dynamics: Improved enhanced sampling and free energy calculation
    Huang, Yu-ming
    McCammon, J. Andrew
    Miao, Yinglong
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2018, 256
  • [3] Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation
    Huang, Yu-ming M.
    McCammon, J. Andrew
    Miao, Yinglong
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2018, 14 (04) : 1853 - 1864
  • [4] Using Multistate Free Energy Techniques to Improve the Efficiency of Replica Exchange Accelerated Molecular Dynamics
    Fajer, Mikolai
    Swift, Robert V.
    McCammon, J. Andrew
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (11) : 1719 - 1725
  • [5] CALCULATION OF SOLVATION FREE-ENERGIES USING A DENSITY FUNCTIONAL/MOLECULAR DYNAMICS COUPLED POTENTIAL
    STANTON, RV
    HARTSOUGH, DS
    MERZ, KM
    JOURNAL OF PHYSICAL CHEMISTRY, 1993, 97 (46): : 11868 - 11870
  • [6] Molecular Dynamics with Very Large Time Steps for the Calculation of Solvation Free Energies
    Abreu, Charlles R. A.
    Tuckerman, Mark E.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2020, 16 (12) : 7314 - 7327
  • [7] Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules
    Oshima, Hiraku
    Re, Suyong
    Sugita, Yuji
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (10) : 5199 - 5208
  • [8] Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems
    Hasse, Timothy
    Huang, Yu-ming M.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2024, 20 (15) : 6485 - 6499
  • [9] Optimization of replica exchange molecular dynamics by fast mimicking
    Hritz, Jozef
    Oostenbrink, Chris
    JOURNAL OF CHEMICAL PHYSICS, 2007, 127 (20):
  • [10] Free energy surfaces of miniproteins with a ββα motif:: Replica exchange molecular dynamics simulation with an implicit solvation model
    Jang, S
    Kim, E
    Pak, Y
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2006, 62 (03) : 663 - 671