GROMOS Tutorial

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

Introduction
Installation Steps
Basic Usage
Advanced Topics