Methods for Monte Carlo simulations of biomacromolecules

A Vitalis, RV Pappu - Annual reports in computational chemistry, 2009 - Elsevier
The state-of-the-art for Monte Carlo (MC) simulations of biomacromolecules is reviewed.
Available methodologies for sampling conformational equilibria and associations of …

On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

M Christen, WF Van Gunsteren - Journal of computational …, 2008 - Wiley Online Library
Methods to search for low‐energy conformations, to generate a Boltzmann‐weighted
ensemble of configurations, or to generate classical‐dynamical trajectories for molecular …

Unified approach for molecular dynamics and density-functional theory

R Car, M Parrinello - Physical review letters, 1985 - APS
We present a unified scheme that, by combining molecular dynamics and density-functional
theory, profoundly extends the range of both concepts. Our approach extends molecular …

[BUCH][B] The equilibrium theory of inhomogeneous polymers

G Fredrickson - 2006 - books.google.com
The Equilibrium Theory of Inhomogeneous Polymers provides an introduction to the field-
theoretic methods and computer simulation techniques that are used in the design of …

Configurational bias Monte Carlo: a new sampling scheme for flexible chains

JI Siepmann, D Frenkel - Molecular Physics, 1992 - Taylor & Francis
We propose a novel approach that allows efficient numerical simulation of systems
consisting of flexible chain molecules. The method is especially suitable for the numerical …

Brownian dynamics as smart Monte Carlo simulation

PJ Rossky, JD Doll, HL Friedman - The Journal of Chemical Physics, 1978 - pubs.aip.org
A new Monte Carlo simulation procedure is developed which is expected to produce more
rapid convergence than the standard Metropolis method. The trial particle moves are chosen …

Optimal tuning of the hybrid Monte Carlo algorithm

A Beskos, N Pillai, G Roberts, JM Sanz-Serna, A Stuart - 2013 - projecteuclid.org
We investigate the properties of the hybrid Monte Carlo algorithm (HMC) in high dimensions.
HMC develops a Markov chain reversible with respect to a given target distribution Π using …

[BUCH][B] Applications of the Monte Carlo method in statistical physics

A Baumgärtner, K Binder, JP Hansen, MH Kalos… - 2013 - books.google.com
Applications of the Monte Carlo method in statistical physics Page 1 Applications of the
Monte-Carlo Method in Statistical Physics KURT BINDER XXXVI Springer Page 2 Topics in …

Simulation of polyethylene above and below the melting point

JJ de Pablo, M Laso, UW Suter - The Journal of chemical physics, 1992 - pubs.aip.org
Polyethylene at equilibrium is studied by computer simulation. Configuration space is
sampled efficiently by a novel Monte Carlo simulation scheme developed for the study of …