Research Articles
Optimizing Large-Scale Molecular Dynamics Performance: A 2025 Guide for Biomedical Researchers
This guide provides a comprehensive framework for researchers and drug development professionals to optimize molecular dynamics (MD) simulations for large-scale biomedical systems.
A Practical Guide to Selecting Solvent Models for Biomolecular Simulation and Drug Development
This article provides a comprehensive guide for researchers and drug development professionals on selecting appropriate solvent models for computational studies.
Mastering Holonomic Constraints in Molecular Dynamics: From Theory to Drug Discovery Applications
This comprehensive guide explores the fundamental principles and practical implementation of holonomic constraints in molecular dynamics simulations, specifically tailored for researchers and drug development professionals.
Navigating Force Field Inaccuracies: From Foundational Challenges to Advanced Solutions in Biomolecular Simulation
This article provides a comprehensive guide for researchers and drug development professionals on understanding, identifying, and overcoming inaccuracies in molecular force field parameters.
Troubleshooting Energy Minimization in MD Simulations: A Comprehensive Guide for Biomedical Researchers
This article provides a comprehensive framework for understanding and resolving common energy minimization failures in Molecular Dynamics (MD) simulations, a critical step in computational drug discovery and biomolecular modeling.
Capturing Motion: How Molecular Dynamics Simulations Reveal Biomolecular Conformational Changes for Drug Discovery
This article provides a comprehensive overview of the application of Molecular Dynamics (MD) simulations in studying biomolecular conformational changes, a critical process in understanding biological function and enabling structure-based drug...
A Practical Guide to Stress-Strain Analysis Using Molecular Dynamics: From Fundamentals to Biomedical Applications
This article provides a comprehensive guide for researchers and scientists on performing stress-strain analysis using Molecular Dynamics (MD) simulations.
Molecular Dynamics Analysis of Ion Transport in Solid Electrolytes: From Fundamental Mechanisms to Advanced Applications
This article provides a comprehensive overview of how Molecular Dynamics (MD) simulations are revolutionizing the understanding and development of solid electrolytes for advanced battery technologies.
Enhanced Sampling with Replica-Exchange MD: A Comprehensive Guide for Biomolecular Simulation and Drug Discovery
Replica-Exchange Molecular Dynamics (REMD) has emerged as a powerful computational technique to overcome the timescale limitations of conventional molecular dynamics, enabling the study of complex biomolecular processes like protein folding,...
Integrating Molecular Dynamics and Pharmacophore Modeling in Modern Drug Discovery: From Dynamic Insights to Clinical Candidates
This article provides a comprehensive overview of the integration of Molecular Dynamics (MD) simulations and pharmacophore modeling to address critical challenges in structure-based drug discovery.