GROMACS Tutorials

Contents

1. GROMACS Introduction
   1.1 GROMACS Installation
   
2. GROMACS Molecular Dynamics Introduction Tutorial
   2.1 Introduction
   2.2 References
   
3. Generating Protein Topologies, Defining Simulation Box & Solvating System
   3.1 Introduction
   3.2 Simulation Commands
       3.2.1 Cleaning the Input Structure
       3.2.2 Generating a Topology
       3.2.3 Defining the Simulation Box
       3.2.4 Solvating the Simulation Box with Water
       3.2.5 Adding Ions to the Solvated System
   
4. Energy Minimization
   4.1 Introduction
   4.2 Simulation Commands
       4.2.1 Energy minimisation
       4.2.2 Energy minimisation Data Analysis
   4.3 References
   
5. NVT Ensemble Equilibration
   5.1 Introduction
   5.2 Simulation Commands
       5.2.1 Equilibration Run - Temperature (NVT Ensemble Equilibration)
       5.2.2 NVT Ensemble Equilibration Data Analysis
   
6. NPT Ensemble Equilibration
   6.1 Introduction
   6.2 Simulation Commands
       6.2.1 Equilibration Run - Pressure (NPT Ensemble Equilibration)
       6.2.2 NPT Ensemble Equilibration Data Analysis
   
7. Molecular Dynamics (MD) Simulation
   7.1 Introduction
   7.2 Simulation Commands
       7.2.1 MD Simulation
       7.2.2 MD Simulation Post-Processing and VMD Processing
       7.2.3 MD Simulation Data Analysis
   

1. GROMACS Introduction

GROMACS is a versatile molecular dynamics (MD) package primarily used to perform MD simulations on biochemical molecules such as proteins, lipids and nucleic acids that have a lot of complicated bonded interactions. However, because it is extremely fast at calculating the non-bonded interactions that usually dominate simulations, it is increasingly used in research on non-biological systems such as polymers and fluid dynamics.

1.2 GROMACS Installation

1. All commands are for Debian-based distros
2. Check C and C++ compilers versions (gcc --version and g++ --version)
3. If these are not up to date with the latest version, install latest versions via following commands

• sudo apt update
• sudo apt install gcc g++

3. Check CMake version via cmake --version. If it is not version 3.18.4 or later, update via:

• sudo apt update
• sudo apt install cmake

4. Download latest GROMACS tarball
5. Move GROMACS tarball to directory you want to install in

• mv gromacs-2024.2.tar.gz <directory>

6. Extract and decompress GROMACS tarball via:

• tar xfz gromacs-2024.2.tar.gz

7. Install GROMACS via following commands:

• cd gromacs-2024.2 && mkdir build && cd build && cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON && make && make check && sudo make install && source /usr/local/gromacs/bin/GMXRC

8. Install GROMACS tools command on your system via command:

• sudo apt install gromacs