GROMACS-A Molecular Dynamic Approach

Important points:

1.THE STEPS WILL TAKE TIME TO RUN AFTER THIS.

2.HAVE PATIENCE AND DONT PRESS ANYTHING AS IT WILL TERMINATE THE RUN.

3.ONCE THE COMMAND LINE APPEARS CONSIDER THE MD SIMULATION COMPLETED.
4.AFTER THIS YOU CAN SHUT DOWN YOUR SYSTEM

5. NEXT WILL BE THE ANALYSIS PART.

Protein – Ligand Simulation:
GROMACS TUTORIAL FOR PROTEIN-LIGAND COMPLEX SIMULATION

• IMPORTANT POINTS
• To start with protein-ligand simulation it is necessary to have a docked complex.
• Docking can be done by pyrx or autodock. (you can refer to autodock tutorial)

STARTING SIMULATION.
1. Make a folder with any name on linux system.
2. In that folder keep your docked complex.
3. Keep the name of the complex simple such as four letter word.