There is a good QM/MM tutorial which can be found here. However, the tutorial is a bit complex and it's difficult to reproduce the whole tutorial for some missing details. Here, we use a simple system to help beginners to setup a QM/MM simulation step by step.
Before starting this tutorial, we assume that:
Firstly, we create a new directory and save the peptide.pdb under this directory.
Type command: pdb2gmx -f peptide.pdb -p peptide -o peptide -ter
For force field, select 6 (OPLS force field)
For N-terminus type, select 3 (None)
For C-terminus type, select 3 (None)
Then, we obtain the three files: the structural file peptide.gro, the topology file peptide.top and the position restriction file porse.itp.
Here, we don't explain why we should introduce link atoms in QM/MM simulation, you should find the answer by yourself and it isn't a tough work.
Before QM/MM simulation, we should modify the peptide.gro and peptide.top files, and specify which atoms should be included in QM region and specify the QMMM parameters in mdp file.
Step 3. Generate tpr file
Till now, we have prepared all the files for generating the tpr file for simulation.
Type command: grompp -f qmmm.mdp -p qmmm.top -n index.ndx -c qmmm.gro -o peptide.tpr
We obtain the peptide.tpr file. Using this tpr file, we can start QM/MM simulation. Here, we will find two warnings, because the incompleteness of the default force field. Since it's just tutorial to show how to setup a QMMM simulation, we ignored it. However, to setup a meaningful simulation, one need to learn more about molecular simulations, which is out of the scape of this tutorial.