We will now generate a simple system to simulate. Create a simple box of CO₂ molecules using insert-molecules:

gmx insert-molecules -ci co2.pdb -nmol 10 -box 10 10 10 -o box.pdb

We do this because if we attempt to simulate only a single molecule, there are no degrees of freedom and the simulation is effectively conducted at 0 K, so nothing moves. That's not very useful or effective at demonstrating that this model works, so we work with a small test system. Now, update the [ molecules ] section of topol.top to reflect the fact that there are now 10 total CO₂ molecules in the system.

Run energy minimization using this .mdp file.

gmx grompp -f em.mdp -c box.pdb -p topol.top -o em.tpr
gmx mdrun -nt 1 -nb cpu -deffnm em 

The system is very small (50 particles) and thus it does not make sense to try to parallelize the simulation, so only one thread is used.

Now run a short simulation on the system using this .mdp file.

gmx grompp -f md.mdp -c em.gro -p topol.top -o md.tpr
gmx mdrun -nt 1 -nb cpu -deffnm md

The CO₂ molecules float around in space, which is expected but not particularly important. What is important to note is that the geometry of the molecules is constructed correctly in each frame. Additionally, we can verify that the moment of inertia of each molecule was correct using the principal module. For ease of understanding, we can analyze each molecule separately:

gmx make_ndx -f em.gro
...
 > splitres 0
 > q

gmx principal -s md.tpr -f md.trr -n index.ndx
(choose any molecule for analysis when prompted)

The output in moi.dat contains the moment of inertia along the x-, y-, and z-axes. The moment of inertia along the x-axis of CO₂ (along the C=O bonds) is zero, while the values of the moments of inertia along the y- and z-axes are approximately 0.500, which is in perfect agreement with the value calculated before when setting up the topology. Therefore, we conclude that this model of CO₂ adequately reproduces the expected moment of inertia.