integrator timing data for tip3p:ligand and protein:ligand simulations suggests a non-pytorch bottleneck?

[dominicrufa]

while profiling some protein:ligand and solvated ligand simulation times with NNPOPS and openmm-torch (treating the ligand with an ANI2x TorchForce) I noticed that there is a similar slowdown factor in both of the phases. does this mean there is a non-pytorch bottleneck in the integrator/force calculation process?

To be more specific, I am doing the following experiments:

1. solvent MM simulation runs md LangevinIntegrator on a Tip3p solvated ligand given by the first entry of this sdf file
2. solvent MM/ML simulation runs the aforementioned integrator on (1) except the ligand atoms are treated with ANI-2x model with a TorchForce
3. complex MM runs the specified integrator on a Tip3p solvated ligand (from the sdf above) concatenated with this protein
4. complex MM/ML runs MD as in (3), except the ligand atoms are treated with ANI-2x (as in 2).

the plot above shows the wall clock time (y-axis) per 2fs timestep; the x axis is the md iteration step number. the wall clock profiles are shown/labelled for the 4 cases described above.

[peastman]

I don't quite understand what you're showing. What exactly are the different systems you're simulating, and what should I be looking at in the results?