Density of states–based molecular simulations
One of the central problems in statistical mechanics is that of finding the density of states of a
system. Knowledge of the density of states of a system is equivalent to knowledge of its …
system. Knowledge of the density of states of a system is equivalent to knowledge of its …
Fast algorithm to calculate density of states
RE Belardinelli, VD Pereyra - Physical Review E—Statistical, Nonlinear, and …, 2007 - APS
An algorithm to calculate the density of states, based on the well-known Wang-Landau
method, is introduced. Independent random walks are performed in different restricted …
method, is introduced. Independent random walks are performed in different restricted …
Wang-Landau algorithm: A theoretical analysis of the saturation of the error
RE Belardinelli, VD Pereyra - The Journal of chemical physics, 2007 - pubs.aip.org
In this work we present a theoretical analysis of the convergence of the Wang-Landau
algorithm [Phys. Rev. Lett. 86, 2050 (2001)] which was introduced years ago to calculate the …
algorithm [Phys. Rev. Lett. 86, 2050 (2001)] which was introduced years ago to calculate the …
Performances of Wang-Landau algorithms for continuous systems
The relative performances of different implementations of the Wang-Landau method are
assessed on two classes of systems with continuous degrees of freedom, namely, two …
assessed on two classes of systems with continuous degrees of freedom, namely, two …
Analysis of the convergence of the and Wang-Landau algorithms in the calculation of multidimensional integrals
RE Belardinelli, S Manzi, VD Pereyra - … E—Statistical, Nonlinear, and Soft Matter …, 2008 - APS
In this Brief Report, the convergence of the 1∕ t and Wang-Landau algorithms in the
calculation of multidimensional numerical integrals is analyzed. Both simulation methods …
calculation of multidimensional numerical integrals is analyzed. Both simulation methods …
Optimal modification factor and convergence of the Wang-Landau algorithm
C Zhou, J Su - Physical Review E—Statistical, Nonlinear, and Soft …, 2008 - APS
We propose a strategy to achieve the fastest convergence in the Wang-Landau algorithm
with varying modification factors. With this strategy, the convergence of a simulation is at …
with varying modification factors. With this strategy, the convergence of a simulation is at …
Calculation of proteins' total side-chain torsional entropy and its influence on protein–ligand interactions
KH DuBay, PL Geissler - Journal of molecular biology, 2009 - Elsevier
Despite the high density within a typical protein fold, the ensemble of sterically permissible
side-chain repackings is vast. Here, we examine the extent of this variability that survives …
side-chain repackings is vast. Here, we examine the extent of this variability that survives …
Aggregation and crystallization of small alkanes
T Shakirov, W Paul - The Journal of Chemical Physics, 2023 - pubs.aip.org
We present a computer simulation study of the aggregation and ordering of short alkane
chains using a united atom model description. Our simulation approach allows us to …
chains using a united atom model description. Our simulation approach allows us to …
Non-genetic global optimization methods in molecular science: An overview
F Calvo - Computational materials science, 2009 - Elsevier
Global optimization methods that are alternative to evolutionary approaches are reviewed.
Improvements over the well-known simulated annealing algorithm are discussed. Several …
Improvements over the well-known simulated annealing algorithm are discussed. Several …
Statistical temperature molecular dynamics: Application to coarse-grained β-barrel-forming protein models
Recently the authors proposed a novel sampling algorithm,“statistical temperature molecular
dynamics”(STMD)[J. Kim et al, Phys. Rev. Lett. 97, 050601 (2006)], which combines …
dynamics”(STMD)[J. Kim et al, Phys. Rev. Lett. 97, 050601 (2006)], which combines …