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openmm / openmm-cookbook

The OpenMM Cookbook and Tutorials
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Add tutorial for running REST #17

Closed zhang-ivy closed 1 year ago

zhang-ivy commented 1 year ago

Here's my latest draft of a tutorial for building a REST system (using OpenMM) and running a REST simulation (using openmmtools). This is a part of a larger effort to draft OpenMM 8 tutorials for the paper.

Please let me know if anything is unclear or there are any typos. Also note that we will want to rename the notebook once it's finalized.

zhang-ivy commented 1 year ago

@peastman : Thanks so much for the feedback! I've addressed all your comments and pushed my changes.

peastman commented 1 year ago

If this is based on code in perses, would it make sense to show how to do this using perses?

I guess the question is, how would you recommend that someone do this in practice? Would you recommend that they do everything from scratch as shown here? Or would you recommend that they use perses? Whichever approach is preferred, that's what the tutorial should show.

16 is merged, so we now have tutorials folder. Can you move the file there?

zhang-ivy commented 1 year ago

If this is based on code in perses, would it make sense to show how to do this using perses? I guess the question is, how would you recommend that someone do this in practice? Would you recommend that they do everything from scratch as shown here? Or would you recommend that they use perses? Whichever approach is preferred, that's what the tutorial should show.

This tutorial is inspired by a factory in perses, but the perses factory creates REST-capable alchemical systems only, and doesn't allow for REST-capable non-alchemical systems. This tutorial shows how to create the latter, which is much simpler.

I think ideally the code in this tutorial could be moved to openmmtools, but for the time being, I would recommend creating the system from scratch.

peastman commented 1 year ago

Ok, sounds good. In that case, if you just move it to the tutorials folder I think it will be good to merge.

zhang-ivy commented 1 year ago

Just moved the notebook (and made a copy of the required input PDB) in tutorials/. Also added the notebook path to tutorials.md

peastman commented 1 year ago

I think that means it's ready to merge. Thank you!