Coordinating OpenMM 8 tutorials

[jchodera]

I am opening this thread to coordinate contributions to new tutorials for use in the OpenMM 8 paper.

I'll keep this list updated with the discussion below:

• Extend openmm-cookbook to build both tutorials and cookbook recipes (@ijpulidos)
• Add tutorial on computing energy components (@yuanqing-wang) Tutorial: Get energy component breakdown #11
• Add tutorial on setting up a protein:ligand simulation from ML/MM simulations with OpenFF and AMBER force fields (@dominicrufa)

[zhang-ivy]

I will probably write a tutorial for writing a REST system or simulating a protein-protein complex with glycans

[sukritsingh]

I'm happy to contribute a notebook on doing enhanced sampling with OpenMM! I could provide examples of

1. Setting up and running Metadynamics
2. Writing a customIntegrator to do accelerated MD, Gaussian Accelerated MD, etc.
3. Attaching a customCVForce as a harmonic potential for any kind of Umbrella sampling.

However, I recognize that OpenMM 8 is focused a lot on the ML and ML/MM features rather than running enhanced sampling methods. It is fairly easy to set up and run nowadays anyways so happy to help either way! @peastman do you have any thoughts on if this is a good idea? John mentioned to ask you.

[peastman]

That would be great! ML may be the trendy new feature, but enhanced sampling is still a really important tool that lots of people use. Besides, ML makes enhanced sampling even more important, since it's slower to begin with.

[ijpulidos]

@jchodera I know you have shared a code that computes hydration free energies using OpenMM, I could make that one a tutorial for OpenMM 8, does that sound okay?

[jchodera]

@ijpulidos: Yes! It would be great if you could use the hydration free energy phase calculation as the basis for a tutorial. There may be ways to further streamline this to eliminate the need for openmmtools as a dependency.

[viktorbelay]

I can contribute a tutorial for working with systems involving lipid bilayers/membranes. Some examples would be setting up a protein:membrane system in OpenMM, simulating systems set up in CHARMMGUI, and simulating transmembrane substrate permeation events.

[jchodera]

@viktorbelay: Illustrations using CHARMM-GUI would be awesome! I think we still may have some interoperability issues that could be streamlined there...

[sef43]

Hi @ijpulidos @zhang-ivy @sukritsingh @dominicrufa @viktorbelay, I am doing some work to update the OpenMM cookbook and Tutorials, have you been able to make any progress with the tutorials @jchodera has mentioned in this thread?

If you have some work than is partially completed I can help you finish them/ do some of the touching up to get them into a tutorial notebook format!

[zhang-ivy]

My tutorial is not ready yet, but will aim to have a draft ready by next week!

[yuanqing-wang]

Same here!

[zhang-ivy]

@sef43 : I've opened a PR with my draft of a tutorial for building a REST system in OpenMM (also includes code on how to use OpenMMTools to run a REST simulation). Please let me know if you have any feedback.

[yuanqing-wang]

@sef43 Added a tutorial for modifying parameters in OpenMM System. This might be useful for building APIs for machine learning force fields. #18

[yuanqing-wang]

@sef43 I plan to add another one later today illustrating that you can write your own MD functional forms (at least for the bonded part) and benchmark against OpenMM---this turns out to be an interesting challenge we face in machine learning force field construction, as seen in https://github.com/dominicrufa/jax-md and https://github.com/choderalab/espaloma