Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

2010 ◽  
Vol 132 (16) ◽  
pp. 165103 ◽  
Author(s):  
Alfonso De Simone ◽  
Philippe Derreumaux
Keyword(s):  
Molecular Dynamics ◽  
Molecular Weight ◽  
Replica Exchange ◽  
Low Molecular Weight ◽  
Amyloid Peptides ◽  
Replica Exchange Molecular Dynamics ◽  
Explicit Solvent

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 Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields

2021 ◽  
Author(s):  
Brajesh Narayan ◽  
Colm Herbert ◽  
Brian J. Rodriguez ◽  
Bernard R. Brooks ◽  
Nicolae-Viorel Buchete
Keyword(s):  
Molecular Dynamics ◽  
Electric Fields ◽  
Replica Exchange ◽  
Amyloid Peptides ◽  
Replica Exchange Molecular Dynamics
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