This chapter provides a brief overview of using the BioExcel Building Block (biobb) to prepare biomolecular systems for molecular dynamics simulations with GROMACS, starting from PDB file manipulat...

This chapter provides a brief overview of using the molecular dynamics simulations with GROMACS, starting from PDB file manipulation. For detailed instructions and the latest features, please cons...

You are about to learn one of the most powerful programming languages in the world: Python. But don’t worry—we are not going to start with a long, confusing lines of code. In Shapes-to-Scripts, we...

This chapter provides step-by-step instructions for installing Linux (Ubuntu) on Windows using WSL2, accessing the SIUC BigDawg supercomputer, installing and configuring GROMACS for molecular dynam...

This section provides the PowerPoint slides, available as PDFs, for Introduction to the Biophysics of Biomolecules. These materials are intended to support both teaching and learning. 📘 Chapter...

This chapter describe the binary system. 4.1 Introduction Both thermodynamics and statistical mechanics describe the behavior of physical systems that contain an enormous number of degrees of free...

This section provides PowerPoint lecture slides in PDF format, for Thermodynamics and Statistical Mechanics. These materials are intended to support both teachers and students. 📘 Chapter 1- Int...

This chapter provides brief intrudction to molecular dynamics (MD). For detailed information, visit the SIUC Research Computing and Cyberingrastructure and read the official user documentation....

This chapter provides an overview of the protein structure. 4.1 Introduction 4.3 Sequence of a Protein

Amino acids are the fundamental building blocks of proteins, which are essential for the structure and function of all living organisms. This chapter provides an overview of the 20 standard amino a...