Is it possible to add instructions to generate output at the end of the section to help the users understand what was done? maybe print properties of the torch_force ?
In the section
Simulation of alanine dipeptide with ANI-2x using OpenMM-Torch
can the simulation of the pure ANI-2x system save a trajectory. Then ask users to visualise the trajectory.
In the section
Mixed system
clarify that this approach only works for whole ML molecule(s)
prompt the users to download the trajectory mixed_traj.pdb for visualisation.
= Exercises need to be introduced
= stretch goal) Is it possible to ask users to compare trajectories of a low quality MACE model vs a high quality model ? Assuming this translates into visible differences in simulated conformations of the dipeptide.
In section_3/machine_learning_potentials.ipynb
Exporting a PyTorch model for use in OpenMMIn the section
Simulation of alanine dipeptide with ANI-2x using OpenMM-TorchIn the section
Mixed systemclarify that this approach only works for whole ML molecule(s)
prompt the users to download the trajectory mixed_traj.pdb for visualisation.
= Exercises need to be introduced
= stretch goal) Is it possible to ask users to compare trajectories of a low quality MACE model vs a high quality model ? Assuming this translates into visible differences in simulated conformations of the dipeptide.