Adaptive ensemble simulations of biomolecules
Highlights•Adaptive ensemble simulations are high-level algorithms for biomolecular
processes.•Adaptivity can greatly improve the computational efficiency of …
processes.•Adaptivity can greatly improve the computational efficiency of …
Adaptive ensemble biomolecular applications at scale
Recent advances in both theory and methods have created opportunities to simulate
biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble …
biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble …
[HTML][HTML] SSAGES: software suite for advanced general ensemble simulations
Molecular simulation has emerged as an essential tool for modern-day research, but
obtaining proper results and making reliable conclusions from simulations requires …
obtaining proper results and making reliable conclusions from simulations requires …
GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
GENeralized‐Ensemble SImulation System (GENESIS) is a software package for molecular
dynamics (MD) simulation of biological systems. It is designed to extend limitations in system …
dynamics (MD) simulation of biological systems. It is designed to extend limitations in system …
Expanded ensemble and replica exchange methods for simulation of protein-like systems
MK Fenwick, FA Escobedo - The Journal of chemical physics, 2003 - pubs.aip.org
Monte Carlo MC methods1–3 provide a direct route to the thermodynamic properties of
equilibrium systems. However, those that employ conventional Boltzmann sampling are of …
equilibrium systems. However, those that employ conventional Boltzmann sampling are of …
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum …
GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD)
software developed to simulate the conformational dynamics of a single biomolecule, as …
software developed to simulate the conformational dynamics of a single biomolecule, as …
Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
Multiscale and inhomogeneous molecular systems are challenging topics in the field of
molecular simulation. In particular, modeling biological systems in the context of multiscale …
molecular simulation. In particular, modeling biological systems in the context of multiscale …
All-atom generalized-ensemble simulations of small proteins
BS Kinnear, MF Jarrold, UHE Hansmann - Journal of Molecular Graphics …, 2004 - Elsevier
We give an overview of some generalized-ensemble techniques that have proven
successful in all-atom simulations of proteins. We show that these techniques enable …
successful in all-atom simulations of proteins. We show that these techniques enable …
Serial generalized ensemble simulations of biomolecules with self-consistent determination of weights
R Chelli, GF Signorini - Journal of chemical theory and …, 2012 - ACS Publications
Serial generalized ensemble simulations, such as simulated tempering, enhance phase
space sampling through non-Boltzmann weighting protocols. The most critical aspect of …
space sampling through non-Boltzmann weighting protocols. The most critical aspect of …
On the structural convergence of biomolecular simulations by determination of the effective sample size
E Lyman, DM Zuckerman - The journal of physical chemistry B, 2007 - ACS Publications
Although atomistic simulations of proteins and other biological systems are approaching
microsecond timescales, the quality of simulation trajectories has remained difficult to …
microsecond timescales, the quality of simulation trajectories has remained difficult to …