[HTML][HTML] Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms
This paper reviews various enhanced conformational sampling methods and explicit/implicit
solvent/membrane models, as well as their recent applications to the exploration of the …
solvent/membrane models, as well as their recent applications to the exploration of the …
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 …
Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations
The growing interest in the complexity of biological interactions is continuously driving the
need to increase system size in biophysical simulations, requiring not only powerful and …
need to increase system size in biophysical simulations, requiring not only powerful and …
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems
In this paper, we address high performance extreme‐scale molecular dynamics (MD)
algorithm in the GENESIS software to perform cellular‐scale molecular dynamics (MD) …
algorithm in the GENESIS software to perform cellular‐scale molecular dynamics (MD) …
Exploring the minimum-energy pathways and free-energy profiles of enzymatic reactions with QM/MM calculations
Understanding molecular mechanisms of enzymatic reactions is of vital importance in
biochemistry and biophysics. Here, we introduce new functions of hybrid quantum …
biochemistry and biophysics. Here, we introduce new functions of hybrid quantum …
A compression strategy for particle mesh Ewald theory
AC Simmonett, BR Brooks - The Journal of chemical physics, 2021 - pubs.aip.org
Particle Mesh Ewald (PME) has become a standard method for treating long-range
electrostatics in molecular simulations. Although the method has inferior asymptotic …
electrostatics in molecular simulations. Although the method has inferior asymptotic …
Multiple staggered mesh Ewald: Boosting the accuracy of the smooth particle mesh Ewald method
H Wang, X Gao, J Fang - Journal of chemical theory and …, 2016 - ACS Publications
The smooth particle mesh Ewald (SPME) method is the standard method for computing the
electrostatic interactions in the molecular simulations. In this work, we develop the multiple …
electrostatic interactions in the molecular simulations. In this work, we develop the multiple …
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer
Generalized replica exchange with solute tempering (gREST) is one of the enhanced
sampling algorithms for proteins or other systems with rugged energy landscapes. Unlike …
sampling algorithms for proteins or other systems with rugged energy landscapes. Unlike …
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 …
Graphics processing unit acceleration and parallelization of GENESIS for large-scale molecular dynamics simulations
J Jung, A Naurse, C Kobayashi… - Journal of Chemical …, 2016 - ACS Publications
The graphics processing unit (GPU) has become a popular computational platform for
molecular dynamics (MD) simulations of biomolecules. A significant speedup in the …
molecular dynamics (MD) simulations of biomolecules. A significant speedup in the …