GROMOS Tutorial

Complete Guide from Installation to Molecular Dynamics

Introduction

This tutorial will guide you through the installation, configuration, and basic usage of GROMOS. GROMOS is a powerful molecular dynamics simulation package that provides comprehensive tools for simulating biomolecular systems.

Installation Steps

1. System Requirements

  • Linux/Unix system
  • Fortran compiler (GCC 7.0+)
  • 4GB RAM (16GB+ recommended)
  • 1GB disk space (10GB+ recommended)

2. Download and Compilation

# Download GROMOS
wget https://www.gromos.net/downloads/gromos-2023.1.tar.gz
tar -xzf gromos-2023.1.tar.gz
cd gromos-2023.1

# Configure and compile
./configure --prefix=/path/to/install
make -j4
make install

# Set environment variables
echo 'export GROMOS_HOME=/path/to/install' >> ~/.bashrc
echo 'export PATH=$PATH:$GROMOS_HOME/bin' >> ~/.bashrc
source ~/.bashrc

Note: Make sure to replace the installation path with your actual path. Also, ensure you have the necessary permissions to install in the chosen directory.

Basic Usage

1. Prepare Input Files

Create a GROMOS input file (protein.top):

TITLE
Protein in Water
END

SYSTEM
Protein in Water
END

MOLECULETYPE
Protein 1
END

2. Run Energy Minimization

# Energy minimization
gromos -f em.mdp -c protein.gro -p protein.top -o em.tpr
gromos -s em.tpr -c em.gro -e em.edr

3. Run Molecular Dynamics Simulation

# Run NVT ensemble simulation
gromos -f nvt.mdp -c em.gro -p protein.top -o nvt.tpr
gromos -s nvt.tpr -c nvt.gro -e nvt.edr

# Run NPT ensemble simulation
gromos -f npt.mdp -c nvt.gro -p protein.top -o npt.tpr
gromos -s npt.tpr -c npt.gro -e npt.edr

Advanced Topics

1. Free Energy Calculations

GROMOS supports various free energy calculation methods:

  • Thermodynamic integration
  • Free energy perturbation
  • Umbrella sampling
  • Metadynamics

2. Parallel Computing

Using MPI for parallel computing:

# Run molecular dynamics simulation using 4 processes
mpirun -np 4 gromos -s md.tpr -c md.gro -e md.edr

Related Tutorials