Overcoming the sampling problem in force field evaluation via GPU-accelerated multidimensional replica exchange molecular dynamics

被引:0
|
作者
Bergonzo, Christina [1 ]
Henriksen, Niel M. [1 ]
Roe, Daniel R. [1 ]
Swails, Jason M. [2 ]
Roitberg, Adrian E. [2 ]
Cheatham, Thomas E., III [1 ]
机构
[1] Univ Utah, Dept Med Chem, Coll Pharm, Salt Lake City, UT 84112 USA
[2] 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
242-COMP
引用
收藏
页数:1
相关论文
共 25 条
  • [1] GPU-accelerated constant pH and redox potential molecular dynamics with multidimensional replica exchange simulations in amber
    Cruzeiro, Vinicius Wilian
    Roitberg, Adrian
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2019, 257
  • [2] Applications of GPU-accelerated replica exchange molecular dynamic simulations of proteins
    Wang, Kai
    Shirts, Michael R.
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2012, 244
  • [3] ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field
    Zhang, Xiaohua
    Sundram, Shiv
    Oppelstrup, Tomas
    Kokkila-Schumacher, Sara I. L.
    Carpenter, Timothy S.
    Ingolfsson, Helgi I.
    Streitz, Frederick H.
    Lightstone, Felice C.
    Glosli, James N.
    JOURNAL OF CHEMICAL PHYSICS, 2020, 153 (04):
  • [4] Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics
    Kai Wang
    John D. Chodera
    Yanzhi Yang
    Michael R. Shirts
    Journal of Computer-Aided Molecular Design, 2013, 27 : 989 - 1007
  • [5] Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics
    Wang, Kai
    Chodera, John D.
    Yang, Yanzhi
    Shirts, Michael R.
    JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2013, 27 (12) : 989 - 1007
  • [6] Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods
    Roe, Daniel R.
    Bergonzo, Christina
    Cheatham, Thomas E., III
    JOURNAL OF PHYSICAL CHEMISTRY B, 2014, 118 (13): : 3543 - 3552
  • [7] SPONGE: A GPU-Accelerated Molecular Dynamics Package with Enhanced Sampling and AI-Driven Algorithms
    Huang, Yu-Peng
    Xia, Yijie
    Yang, Lijiang
    Wei, Jiachen
    Yang, Yi Isaac
    Gao, Yi Qin
    CHINESE JOURNAL OF CHEMISTRY, 2022, 40 (01): : 160 - 168
  • [8] Multi-Scale Sampling using Temperature Accelerated and Replica Exchange Molecular Dynamics
    Yu, Yamamori
    Kitao, Akio
    BIOPHYSICAL JOURNAL, 2014, 106 (02) : 461A - 461A
  • [9] GPU-accelerated replica exchange molecular simulation on solid-liquid phase transition study of Lennard-Jones fluids
    Nomura, Kentaro
    Oikawa, Minoru
    Kawai, Atsushi
    Narumi, Tetsu
    Yasuoka, Kenji
    MOLECULAR SIMULATION, 2015, 41 (10-12) : 874 - 880
  • [10] 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