Research Articles
Molecular Dynamics Simulations: A Comprehensive Guide to Best Practices from Setup to AI Integration
This article provides a comprehensive guide to best practices in molecular dynamics (MD) simulations, tailored for researchers, scientists, and drug development professionals.
Beyond Force Metrics: A Practical Guide to Improving Stability and Convergence in Molecular Dynamics Simulations
Molecular dynamics (MD) simulations are indispensable in drug discovery and materials science, yet achieving stable and converged results remains a significant challenge.
Classical vs. Reactive MD: A Comprehensive Guide to Force Field Selection for Biomedical Research
This article provides a detailed comparison between Classical Molecular Dynamics (MD) and Reactive Force Fields, with a focus on ReaxFF, tailored for researchers and professionals in drug development and biomedical...
Bridging the Gap: A Comprehensive Guide to Validating Molecular Dynamics Diffusion Coefficients with Experimental Measurements
This article provides a comprehensive framework for researchers, scientists, and drug development professionals seeking to validate diffusion coefficients derived from Molecular Dynamics (MD) simulations against experimental data.
AMBER vs CHARMM vs OPLS: A Comprehensive Guide to Force Field Performance for Biomolecular Simulations
This article provides a systematic comparison of AMBER, CHARMM, and OPLS force fields, essential tools for molecular dynamics simulations in drug discovery and structural biology.
Assessing the Accuracy of MD-Derived Thermodynamic Properties: A Guide for Computational Researchers and Drug Developers
Molecular dynamics (MD) simulations have become an indispensable tool for predicting thermodynamic properties critical to drug design and materials science, such as binding free energy, entropy, and enthalpy.
Explicit vs. Implicit Solvent Models in MD Simulations: A Comprehensive Guide for Computational Researchers
This article provides a systematic comparison of explicit and implicit solvent models in molecular dynamics (MD) simulations, tailored for researchers and professionals in computational biophysics and drug development.
Validating Molecular Dynamics Simulations with Experimental NMR Data: A Comprehensive Guide for Biomedical Research
This article provides a comprehensive framework for validating Molecular Dynamics (MD) simulations using experimental Nuclear Magnetic Resonance (NMR) data, a critical synergy for advancing structural biology and rational drug design.
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.