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
  • [21] Optimizing replica exchange moves for molecular dynamics
    Nadler, Walter
    Hansmann, Ulrich H. E.
    PHYSICAL REVIEW E, 2007, 76 (05)
  • [22] Online Optimization of Total Acceptance in Hamiltonian Replica Exchange Simulations
    MacCallum, Justin L.
    Muniyat, Mir Ishruna
    Gaalswyk, Kari
    JOURNAL OF PHYSICAL CHEMISTRY B, 2018, 122 (21): : 5448 - 5457
  • [23] Multi-Scale Sampling using Temperature Accelerated and Replica Exchange Molecular Dynamics
    Yu, Yamamori
    Kitao, Akio
    BIOPHYSICAL JOURNAL, 2014, 106 (02) : 461A - 461A
  • [24] 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
  • [25] Free energy calculations for DNA base stacking by replica-exchange umbrella sampling
    Murata, K
    Sugita, Y
    Okamoto, Y
    CHEMICAL PHYSICS LETTERS, 2004, 385 (1-2) : 1 - 7
  • [26] Replica exchange molecular dynamics simulations of reversible folding
    Rao, F
    Caflisch, A
    JOURNAL OF CHEMICAL PHYSICS, 2003, 119 (07): : 4035 - 4042
  • [27] Replica Exchange Statistical Temperature Molecular Dynamics Algorithm
    Kim, Jaegil
    Straub, John E.
    Keyes, Tom
    JOURNAL OF PHYSICAL CHEMISTRY B, 2012, 116 (29): : 8646 - 8653
  • [28] Error and efficiency of replica exchange molecular dynamics simulations
    Rosta, Edina
    Hummer, Gerhard
    JOURNAL OF CHEMICAL PHYSICS, 2009, 131 (16):
  • [29] Microcanonical replica exchange molecular dynamics simulation of proteins
    Kar, Parimal
    Nadler, Walter
    Hansmann, Ulrich H. E.
    PHYSICAL REVIEW E, 2009, 80 (05):
  • [30] Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations
    Rosta, Edina
    Buchete, Nicolae-Viorel
    Hummer, Gerhard
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2009, 5 (05) : 1393 - 1399