I resolved this issue.
Here’s the solution:
I edited my mdrun command to include -update gpu. Thus, the full command is as follows:
gmx mdrun -s test.tpr -v -x test.xtc -c test.gro -nb gpu -bonded gpu -pme gpu -nstlist 400
This aligns with the suggestions from this NVIDIA blog.
I initially did not include the -update gpu argument because I was using the Nose-Hoover themostat, which for whatever reason does not work with the -update argument. Because I was not committed to Nose-Hoover for any particular reason besides aligning with prior studies, I have opted to use the v-rescale thermostat in my .mdp file (as suggested here). v-rescale works with the -update gpu argument in mdrun.
The simulation now runs in the expected time, i.e., ~30 hours. So matter resolved.
