GROMACS Tutorial

Introduction

GROMACS is a versatile package for performing molecular dynamics simulations and energy minimization. This tutorial will guide you through the basic usage of GROMACS.

Installation Steps

Windows

1. Download the Windows installer from the official website
2. Run the installer and follow the installation wizard
3. Add GROMACS to your system PATH

Linux

1. Install required dependencies:

   sudo apt-get install cmake gcc g++

2. Download and extract GROMACS source code
3. Configure and compile:

   mkdir build
   cd build
   cmake .. -DGMX_BUILD_OWN_FFTW=ON
   make
   sudo make install

macOS

1. Install Homebrew if not already installed
2. Install GROMACS using Homebrew:

   brew install gromacs

Basic Usage

Preparing Input Files

1. Prepare protein structure file (PDB format)
2. Generate topology file:

   gmx pdb2gmx -f protein.pdb -o processed.gro -water spce

3. Define simulation box:

   gmx editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt cubic

4. Add solvent:

   gmx solvate -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top

Energy Minimization

1. Prepare energy minimization parameters
2. Run energy minimization:

   gmx grompp -f em.mdp -c solv.gro -p topol.top -o em.tpr
   gmx mdrun -v -deffnm em

Molecular Dynamics Simulation

1. Prepare MD parameters
2. Run MD simulation:

   gmx grompp -f md.mdp -c em.gro -p topol.top -o md.tpr
   gmx mdrun -v -deffnm md

Advanced Topics

Analysis Tools

• RMSD analysis
• RMSF analysis
• Secondary structure analysis
• Energy analysis

Performance Optimization

• GPU acceleration
• Parallel computing
• Memory optimization