Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm

2004 ◽  
pp. 119-149 ◽  
Author(s):  
Hugh Nymeyer ◽  
S. Gnanakaran ◽  
Angel E. García
Keyword(s):  
Protein Folding ◽  
Replica Exchange ◽  
Exchange Algorithm ◽  
Atomic Simulations

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

2016 ◽  
Vol 18 (18) ◽  
pp. 13052-13065 ◽  
Author(s):  
Emanuel K. Peter ◽  
Joan-Emma Shea ◽  
Igor V. Pivkin
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Protein Folding ◽  
Kinetic Monte Carlo ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Accelerated Simulation ◽  
Explicit Solvent ◽  
Exchange Algorithms

In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC).

scholarly journals Simulating replica exchange simulations of protein folding with a kinetic network model

2007 ◽  
Vol 104 (39) ◽  
pp. 15340-15345 ◽  
Author(s):  
W. Zheng ◽  
M. Andrec ◽  
E. Gallicchio ◽  
R. M. Levy
Keyword(s):  
Protein Folding ◽  
Network Model ◽  
Replica Exchange

Surface aided replica exchange algorithm applied to the prewetting transition

2010 ◽  
Vol 108 (11) ◽  
pp. 1539-1543 ◽  
Author(s):  
Stephanie Nieves-Torres ◽  
Gustavo E. López
Keyword(s):  
Replica Exchange ◽  
Exchange Algorithm

Greedy replica exchange algorithm for heterogeneous computing grids

2015 ◽  
Vol 21 (9) ◽  
Author(s):  
Christopher Lockhart ◽  
James O’Connor ◽  
Steven Armentrout ◽  
Dmitri K. Klimov
Keyword(s):  
Heterogeneous Computing ◽  
Replica Exchange ◽  
Exchange Algorithm
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