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...

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

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....

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...

This chapter provides a brief desribtion of water molecules that required for biochemical reaction. 2.1 Introduction Solvents play a fundamental role in biochemical reactions by providing the medi...

Understanding the three-dimensional structures of biomolecules is essential for advancing our knowledge in diverse fields—from drug discovery to the computational modeling of complex biological pro...

This chapter provides a brief overview of Protein Data Bank (PDB) files, which are a standard format for storing information about the three-dimensional structures of biological molecules, such as ...

This chapter provides a brief overview of key events and concepts that have shaped the field of biophysics. We believe that understanding these historical developments is crucial for appreciating t...

This chapter provides a brief overview of using the CHARMM-GUI to prepare biomolecular systems for molecular dynamics simulations with GROMACS, starting from PDB file manipulation. For detailed in...

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...