Complete Guide from Installation to Molecular Dynamics
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.
# 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.
Create a GROMOS input file (protein.top):
TITLE
Protein in Water
END
SYSTEM
Protein in Water
END
MOLECULETYPE
Protein 1
END
# 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
# 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
GROMOS supports various free energy calculation methods:
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
Molecular Dynamics
Molecular Dynamics
Molecular Dynamics