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Related Experiment Video

Updated: Feb 26, 2026

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple

Chigusa Kobayashi¹, Jaewoon Jung^1,2, Yasuhiro Matsunaga^1,3

¹Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamachi, Chuo-ku, Kobe, 650-0047, Japan.

Journal of Computational Chemistry

|July 19, 2017

Summary

The GENeralized-Ensemble SImulation System (GENESIS) 1.1 software enhances molecular dynamics simulations for biological systems. It offers improved performance and advanced algorithms for conformational sampling and free-energy calculations.

Keywords:

graphics processing unit molecular dynamics multiple time step integration replica exchange molecular dynamics string method

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Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Area of Science:

Computational biology
Biophysics
Molecular modeling

Background:

The GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulations of biological systems.
Existing limitations in system size and accessible timescales necessitate advanced simulation techniques.

Discussion:

GENESIS 1.1 incorporates new functions and algorithms to overcome current limitations in MD simulations.
The integration of AMBER, GROMACS, and CHARMM energy functions expands the applicability of GENESIS.
Optimized performance through multiple time-step integration and hybrid (CPU+GPU) computing accelerates complex simulations.

Key Insights:

GENESIS 1.1 supports a wider range of potential energy functions, including all-atom and coarse-grained models.
Enhanced conformational sampling algorithms, such as the string method and replica-exchange umbrella sampling, are implemented.
The software facilitates the determination of minimum free-energy pathways and free-energy profiles for macromolecular conformational changes.

Outlook:

The updated GENESIS 1.1 software provides a more powerful and versatile platform for biological research.
Future developments may focus on further scaling and integration with experimental data.
Continued advancements in computational power and algorithms will enhance the scope of achievable simulations.