GROMACS [1] offers a vast range of functions when it comes to molecular dynamics simulation. Today, we are going to explore it for the simulation of small organic molecules.Contents1. Obtaining the molecule structure2. Preparing force field3. Preparing the molecule4. Generating topology of the molecule5. Defining box6. Solvating the molecule7. Energy Minimization8. Running MD SimulationReferences In … Continue reading Tutorial: MD Simulation of small organic molecules using GROMACS