Not only querying, but also modifying system parameters #18

yuanqing-wang · 2023-04-19T03:38:00Z

Modifying Parameters in System

in the same manner as in Espaloma

yuanqing-wang · 2023-04-19T03:48:41Z

cross-ref: #12

peastman

These notebooks have a lot of overlap with existing ones. There's already a cookbook entry on inspecting system parameters. Is there a good reason to have two on the same thing? The other notebook is esoteric and sort of out of scope: using OpenMM to validate your own MD code that you've written separately. Mostly that isn't about OpenMM. The only part that's really about OpenMM is the discussion of how to query energy components, but we already have a cookbook entry on that.

peastman · 2023-04-19T19:08:40Z

notebooks/cookbook/Modifying Parameters in an OpenMM System.ipynb

+    "Some machine learning force field construction schemes, such as [Espaloma](https://pubs.rsc.org/en/content/articlehtml/2022/sc/d2sc02739a), would output parameters which can be picked up by the parameter-holding `System` object of OpenMM, which could be further used in molecular dynamics (MD) simulations just like a vanilla `System`.\n",
+    "In this tutorial, we show how you can modify the parameters of `System` object so you can write your own machine learning force field API.\n",
+    "\n",
+    "This example is inspired by the [Espaloma deployment](https://github.com/choderalab/espaloma/blob/master/espaloma/graphs/deploy.py) implementation."


This description is overly specific. Nothing in this notebook is really specific to machine learning. You're just showing how to examine and change the parameters in a System. How about something like this?

Sometimes it is useful to examine the parameters in a System. For example, you might want to check what parameters a ForceField has assigned to a particular bond or angle. In other cases you may want to modify those parameters to make a bond behave differently from what the ForceField assigned.

notebooks/cookbook/Modifying Parameters in an OpenMM System.ipynb

yuanqing-wang · 2023-04-20T01:43:22Z

@peastman how about I get rid of the separate "modify the parameters" one and simply append the existing "query the parameters" tutorial with ways to modify them in-place.

For the other one, I have seen so many people trying to using OpenMM to benchmark their own MM implementations. I feel like the community would benefit from a tutorial.

yuanqing-wang · 2023-04-20T06:48:43Z

see 38035e4 where I combined the modifying parameter tutorial with the querying parameter tutorial

yuanqing-wang · 2023-04-23T12:42:06Z

would love your feedback! @peastman @sef43

Perhaps the second item is more suitable for a tutorial than a cookbook?

notebooks/cookbook/Querying and Modifying Charges and Other Parameters.ipynb

sef43 · 2023-04-24T12:35:41Z

I think the setting different parameters is a good addition to the existing cookbook entry!

I think as you have suggested the notebook for "Use OpenMM to Verify Your MM Functional Form Implementation" should be a separate tutorial. Can you remove it from this PR and make a new PR adding that as a tutorial, we can then review it properly in the new PR.

… again

yuanqing-wang · 2023-04-25T04:24:06Z

@sef43 I've made the changes as requested. Will follow up with another PR for the separate notebook.

yuanqing-wang · 2023-04-25T04:44:58Z

Separated PR here: #22

peastman

Looks good! I made a few very minor suggestions.

notebooks/cookbook/Querying and Modifying Charges and Other Parameters.ipynb

peastman · 2023-04-25T18:12:52Z

I just realized it's missing one very important part. Let's add the following at the end.

Modifying Force objects will affect any new Simulations or Contexts you create, but it will have no effect on ones that already exist. If you want your modifications to apply to an existing Simulation, you can copy them over by calling bonded.updateParametersInContext(simulation.context).

yuanqing-wang · 2023-04-26T05:32:50Z

@peastman I've made the changes per your suggestions. I've also added the code to modify existing Context.

notebooks/cookbook/Querying and Modifying Charges and Other Parameters.ipynb

peastman · 2023-04-27T00:25:20Z

notebooks/cookbook/Querying and Modifying Charges and Other Parameters.ipynb

+    "        bonded.setBondParameters(\n",
+    "            i, particle1, particle2, length, \n",
+    "            2666 * unit.kilojoules_per_mole/unit.nanometer**2\n",
+    "        )"


No need to split this onto four lines. It makes the code less readable, and it can easily fit on a single line.

Sure! If we don't worry about the 80 char limit.

If someone wants to view the entry on a VT52 terminal, I admit it will be inconvenient. But I think we can say VT100 is the earliest terminal we support. :)

yuanqing-wang · 2023-04-28T03:43:20Z

I've updated the PR accordingly.

peastman · 2023-04-30T21:39:57Z

Just one unnecessary line that still needs to be removed. Then I think it will be ready to merge.

yuanqing-wang · 2023-05-01T20:47:31Z

Just one unnecessary line that still needs to be removed. Then I think it will be ready to merge.

Sorry which unnecessary line?

peastman · 2023-05-01T21:15:40Z

bonded = [f for f in system.getForces() if isinstance(f, HarmonicBondForce)][0]

peastman · 2023-05-01T22:21:30Z

Looks good. Thanks!

Modifying parameter

6a01959

in the same manner as in Espaloma

yuanqing-wang mentioned this pull request Apr 19, 2023

Coordinating OpenMM 8 tutorials #12

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yuanqing-wang changed the title ~~Add OpenMM tutorials~~ Add OpenMM tutorials for APIs of machine learning force field constructions Apr 19, 2023

yuanqing-wang and others added 7 commits April 19, 2023 14:24

title change

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start implementing own functional forms

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get energy components

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trash clean

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Merge branch 'main' of https://github.com/yuanqing-wang/openmm-cookbook

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Update Use OpenMM to Verify Your MM Functional Form Implementation.ipynb

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trash cleaning

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peastman reviewed Apr 19, 2023

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merged modifying parameters into querying parameters

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yuanqing-wang requested a review from peastman April 21, 2023 17:30

sef43 suggested changes Apr 24, 2023

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yuanqing-wang added 2 commits April 25, 2023 12:21

moved benchmarking script into another PR; fixed typo; added querying…

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… again

Merge branch 'openmm:main' into main

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yuanqing-wang changed the title ~~Add OpenMM tutorials for APIs of machine learning force field constructions~~ Not only querying, but also modifying system parameters Apr 25, 2023

yuanqing-wang requested a review from sef43 April 25, 2023 04:24

yuanqing-wang mentioned this pull request Apr 25, 2023

Tutorial: Get energy component breakdown #11

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peastman reviewed Apr 25, 2023

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Use OpenMM to Verify Your MM Functional Form Implementation.ipynb #22

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minor fixes; update parameters in Context

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peastman reviewed Apr 27, 2023

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remove line char limit; get rid of Context

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peastman merged commit 83334ce into openmm:main May 1, 2023

sef43 mentioned this pull request May 2, 2023

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Not only querying, but also modifying system parameters #18

Not only querying, but also modifying system parameters #18

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Not only querying, but also modifying system parameters #18

Not only querying, but also modifying system parameters #18

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