The molecular dynamics guides I wish I’d had when I started

What to type, which files you need, and why each step matters: pick a path below, or start here if you are new.

GROMACS: From Theory to Simulation, the complete protein-in-water guide

Learn the theoryForce fields, integrators, ensembles, thermostats, periodic boundary conditions. Run your first simulationInstall GROMACS, file formats, the .mdp file, a full protein-in-water walkthrough. Analyse a trajectoryRMSD, RMSF, SASA, hydrogen bonds and clustering, each with a plotting example. Visualize your resultsPublication-quality figures in PyMOL, trajectory inspection in VMD.

Latest articles

An Introduction to Enhanced Sampling and Metadynamics

published on 05/18/2024 included in category Molecular Dynamics and series MD Theory Series

An Introduction to Enhanced Sampling with a focus on Metadynamics simulations

VMD Selection Tool: syntax, keywords, and examples for selecting atoms and residues

published on 03/24/2024 included in category Visualization and series VMD Analysis Series

Master VMD selections: select atoms by index, name, or element; residues by number or name; and use within, and, or, not for complex criteria.

Rowan - Next-Generation Quantum Chemistry

published on 01/29/2024 included in category GROMACS

Experience quantum chemistry simplified with Rowan – the next-gen platform making molecular visualization accessible. Register now for 500 free credits!

VMD Representations and Color Schemes

published on 01/04/2024 included in category Visualization and series VMD Analysis Series

Explore drawing methods, color schemes, and atom-specific adjustments in VMD.

Scripting in PyMOL: A Comprehensive Guide for Beginners

published on 10/15/2023 included in category Visualization and series PyMOL Beginner Series

Learn how to automate tasks and optimize image generation in PyMOL using pml and Python scripting.

GROMACS Tutorial: Coarse-Grained simulation of a protein membrane system

published on 09/05/2023 included in category GROMACS and series Coarse-Grained Simulations

Using GROMACS to perform Coarse-Grained (CG) simulations of a protein in a membrane environment using the Martini force field

Hydrogen bond Analysis with VMD

published on 08/05/2023 included in category Visualization and series VMD Analysis Series

A Guide to the Hydrogen Bond extension to analyze hbonds using VMD

RMSD Analysis in VMD: how to calculate and plot RMSD from a trajectory

published on 07/23/2023 included in category Visualization and series VMD Analysis Series

Learn how to calculate RMSD in VMD using the RMSD Trajectory Tool. Covers loading your trajectory, aligning to a reference structure, computing per-frame RMSD, and plotting the results to assess simulation stability.

GROMACS Tutorial: Coarse-Grained Simulations with Martini 3 Force Field

published on 07/02/2023 included in category GROMACS and series Coarse-Grained Simulations

Using GROMACS to perform Coarse Grained simulations of a soluble protein with Martini force field

VMD Measurements: Analyze Distances and Angles with VMD

published on 06/10/2023 included in category Visualization and series VMD Analysis Series

Use VMD to measure distances and angles, and track their progression in molecular simulations.