MD Tutorials
On this site, you will find tutorials I have written for various molecular dynamics programs. This site is still very much under construction, so please check back frequently for updates.
Lysozyme in Water - MD Tutorials
Each step will contain an explanation of input and output, using typical settings for general use. This tutorial assumes you are using a GROMACS version in the 2025.x series. It was …
Protein-Ligand Complex - MD Tutorials
This tutorial focuses specifically on issues related to dealing with the ligand, assuming that the user is familiar with basic GROMACS operations and the contents of a topology.
GROMACS Tutorials
BASIC TUTORIALSADVANCED TUTORIALS
KALP-15 in DPPC - MD Tutorials
This tutorial assumes you are using GROMACS version 2018 or newer. Please note that the purpose of this tutorial is instructional, to build a membrane protein system and also to …
Protein-Ligand Complex - MD Tutorials
Protein-Ligand ComplexGROMACS Tutorial Step Two: Prepare the Ligand Topology
Lysozyme in Water - MD Tutorials
For this tutorial, a few basic tools will be introduced. The first is trjconv, which is used as a post-processing tool to strip out coordinates, correct for periodicity, or manually alter the trajectory …
Lysozyme in Water - MD Tutorials
For this tutorial, we will utilize hen egg white lysozyme (PDB code 1AKI). Go to the RCSB website and download the PDB text for the crystal structure. Once you have downloaded the structure, …
Protein-Ligand Complex - MD Tutorials
Analyzing Protein-Ligand Interactions and Ligand Dynamics This tutorial cannot possible cover all analysis methods that you may wish to perform. A few basic operations will be illustrated here. …
Building Biphasic Systems - MD Tutorials
The purpose of this tutorial is to guide the user through the process of building a heterogeneous biphasic system composed of hydrophobic (cyclohexane) and hydrophilic (water) layers.