scholarly journals Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

2014 ◽  
Vol 10 (3) ◽  
pp. 1341-1352 ◽  
Author(s):  
Jason M. Swails ◽  
Darrin M. York ◽  
Adrian E. Roitberg
Keyword(s):  
Molecular Dynamics ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Constant Ph ◽  
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 Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation

2018 ◽  
Vol 149 (7) ◽  
pp. 072338 ◽  
Author(s):  
Vinícius Wilian D. Cruzeiro ◽  
Marcos S. Amaral ◽  
Adrian E. Roitberg
Keyword(s):  
Molecular Dynamics ◽  
Redox Potential ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Constant Ph
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