Monte Carlo vs Molecular Dynamics for All-Atom Polypeptide Folding Simulations

2006 ◽  
Vol 110 (33) ◽  
pp. 16733-16742 ◽  
Author(s):  
Jakob P. Ulmschneider ◽  
Martin B. Ulmschneider ◽  
Alfredo Di Nola
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Polypeptide Folding ◽  
Folding Simulations

Numerical Methods for the Kinetic Theory of Fluids

2018 ◽  
Author(s):  
Sauro Succi
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Numerical Methods ◽  
Kinetic Theory ◽  
Computational Efficiency ◽  
Lattice Boltzmann ◽  
Direct Simulation Monte Carlo ◽  
Particle Methods ◽  
Direct Simulation ◽  
Simulation Monte Carlo

This chapter provides a bird’s eye view of the main numerical particle methods used in the kinetic theory of fluids, the main purpose being of locating Lattice Boltzmann in the broader context of computational kinetic theory. The leading numerical methods for dense and rarified fluids are Molecular Dynamics (MD) and Direct Simulation Monte Carlo (DSMC), respectively. These methods date of the mid 50s and 60s, respectively, and, ever since, they have undergone a series of impressive developments and refinements which have turned them in major tools of investigation, discovery and design. However, they are both very demanding on computational grounds, which motivates a ceaseless demand for new and improved variants aimed at enhancing their computational efficiency without losing physical fidelity and vice versa, enhance their physical fidelity without compromising computational viability.

Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensemble

1996 ◽  
Vol 259 (3-4) ◽  
pp. 321-330 ◽  
Author(s):  
Ulrich H.E. Hansmann ◽  
Yuko Okamoto ◽  
Frank Eisenmenger
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Monte Carlo Simulations

Magnetic relaxation of xenon‐131 dissolved in benzene. A study by molecular dynamics and Monte Carlo simulations

1993 ◽  
Vol 98 (2) ◽  
pp. 1566-1578 ◽  
Author(s):  
M. Luhmer ◽  
D. van Belle ◽  
J. Reisse ◽  
M. Odelius ◽  
J. Kowalewski ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Magnetic Relaxation

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).

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