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).

An adaptive bias – hybrid MD/kMC algorithm for protein folding and aggregation

2017 ◽  
Vol 19 (26) ◽  
pp. 17373-17382 ◽  
Author(s):  
Emanuel K. Peter ◽  
Joan-Emma Shea
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Protein Folding ◽  
Kinetic Monte Carlo ◽  
Explicit Solvent

We present a novel hybrid Molecular Dynamics/kinetic Monte Carlo (MD/kMC) algorithm based on a dynamical redefinition of biases throughout the simulation. This algorithm is applied to the study of protein folding and aggregation in explicit solvent.

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