Learn Molecular Dynamics from Scratch

Discover molecular dynamics through computer simulations that model how atoms and molecules interact over time and space to produce results, without requiring programming languages or operating systems, using supercomputing resources.

Learn what a force field is and how it governs energy, bond lengths, angles, and electrostatic and other interactions in molecular dynamics simulations.

Discover why GROMACS stands out as a fast, flexible, open-source molecular dynamics package, with regular updates, tutorials, and a supportive user forum.

Learn how to install Ubuntu on Windows via the Windows Subsystem for Linux, enable required features, install from the Microsoft Store, and configure the first user.

Learn how to install Gromacs on Windows os, updating the system, installing required libraries and compilers, configuring cmake, building from source, and verifying the installation.

Learn about the different GROMACS file formats, including input files, topology files with forcefields, and parameter sets; understand how these combine to produce coordinates, velocities, and energy data.

Learn molecular dynamics from scratch by sourcing PDB files from the protein data bank, cleaning headers and water, converting proteins to compact formats, and preparing files for MD simulations.

Learn how to perform energy minimization in molecular dynamics by neutralizing the system, adding ions, and analyzing the potential energy graph to verify proper minimization.

Learn how to properly calibrate a molecular dynamics system for accurate simulations by using NVT and NPT ensembles, focusing on temperature and pressure control during equilibration.