How to Validate Molecular Dynamics Simulation Results Before Publishing 14 min read Intermediate Running an MD simulation is the beginning, not the end. Before any result from a trajectory can be reported, it must pass a series of validation checks — not optional best practices, but the minimum standard that reviewers at major journals expect…
10 Common Molecular Dynamics Simulation Mistakes (And How to Avoid Every One) 13 min read All levels Most failed MD simulations don’t fail with an obvious error message. They run to completion, produce a plausible-looking trajectory, and return results you might trust — until someone more experienced looks at your methods. These are the ten…
MM-GBSA Tutorial: How to Calculate Binding Free Energy After Molecular Dynamics 13 min read Intermediate Docking scores are estimates. MM-GBSA is the next level up — a physics-based method that uses your MD trajectory to calculate binding free energy significantly more accurately. This tutorial explains what it is, why it’s better than docking scores, and…
Protein-Ligand Molecular Dynamics Simulation in GROMACS: Parameterize, Run and Analyze 18 min read Intermediate Protein-only MD is the foundation. Protein-ligand MD is where it gets useful for drug discovery — validating docking results, characterizing binding stability, and calculating binding free energies. The extra complexity is almost entirely in Step 1: getting force field parameters for…
How to Visualize MD Trajectories in VMD and PyMOL: Complete Tutorial 13 min read Beginner to intermediate Running an MD simulation without visualizing the trajectory is like developing film without looking at the photos. This tutorial covers everything you need to load, navigate, clean up, and render your trajectory in both VMD and PyMOL —…
How to Analyze Molecular Dynamics Results: RMSD, RMSF, Radius of Gyration and Hydrogen Bonds 18 min read Intermediate A finished MD trajectory is raw data — gigabytes of atomic coordinates that mean nothing until you calculate something from them. This tutorial covers the four most important analysis metrics, how to compute each with GROMACS, how…
How to Choose a Force Field for MD Simulation: AMBER vs CHARMM vs GROMOS vs OPLS 14 min read Intermediate Force field choice is one of the most consequential decisions in molecular dynamics simulation — and one of the most consistently glossed over in beginner tutorials. This guide explains what force fields actually are, how…
GROMACS Tutorial for Beginners: Run Your First MD Simulation From Scratch (2026) 22 min read Complete beginner By the end of this tutorial you will have run a complete molecular dynamics simulation — protein prepared, equilibrated, production MD completed, and basic analysis done. Every command is exact and explained. No prior MD experience required. Contents…
How to Prepare a Protein for Molecular Dynamics Simulation: Complete GROMACS Guide 18 min read Beginner to intermediate System preparation is where most MD simulations succeed or fail — and where most beginners spend the most time stuck. This tutorial walks through every step from a raw PDB file to a simulation-ready system, with exact…
How to Install GROMACS on Linux, Mac and Windows (2026 Guide) 13 min read Complete beginner GROMACS runs from the command line — there’s no installer to double-click. This guide walks through every installation method across all three platforms, with exact commands, what the output should look like, and fixes for the errors most beginners…