Follow-up workshops are the riskiest kind of demo - They’re LIVE software demos, and we want invite you to be running run it on your own machine as well. These are intended to be hands-on and technical, so we’ll be discussing both the relevant science and technical aspects of using the tools.
This will be recorded, but recording will stop after the end of the notebook Q&A.Feel free to ask questions via voice or chat during the workshop . There is no expectation of privacy in this meeting,either in the recorded or unrecorded parts, so assume it is a public spaceeven after the recording finishes.General plan is for this to be a bit more than one hour about two hours of prepared material, feel free to interrupt with questions, and if we have a natural stopping point we might take a 5 minute break. After the prepared material we’ll have a developer support session, where we
turn off the recording andencourage you to try feeding your own data in or modify the workflow to your liking. During that time we can help out with any problems you encounter.Start the install instructions immediately if you haven’t already -The installation instructions are available on the workshop page, but if you’re not able to install the material for this one locally, you might be best off just following and running yourself later. If you’re having trouble, please mention it in the Zoom chat and switch to the Colab link available on the project page. OpenFF developers will work with you during the dev time to debug your setup.
2024_04_24 Vignettes Workshop
MT and JW will prepare personal meeting links and stage them here
JW – https://us06web.zoom.us/j/83259717547?pwd=ke1l7YiR1UGxTOI1zkFW9Ydorb5hH8.1
MT – https://us06web.zoom.us/j/87885784973?pwd=gnIHcbboXbxdopbG3OBb9kyoUKUYLr.1
Main meeting link - https://us06web.zoom.us/j/87885784973?pwd=gnIHcbboXbxdopbG3OBb9kyoUKUYLr.1
Participants
Audrius Kalpokas
Cesar
Eva Notari
Jeff Wagner
John
Josh Mitchell
Luke Zondagh
Matt Thompson
Noora
Pavel Buslaev
Vaclav Hanzl
Vedran Miletic
Vsites
PB – AFAIK, different engines support different vsites. How are you planning to support these in the future?
JM – We will pick the appropriate representation for our SMIRNOFF vsites in other engines. But some engines won’t be able to handle them, those will emit an error when you try to export them in Interchange.
PB – Will you have two lines of FF, one with vsites, another without?
JW – In the distant future, we’ll only have a single FF line that will include vsites. But we won’t include them until we show that they’re worth the performance hit. If it turns out that there’s a type of vsite that improves FF performance a lot and ISN’T supported by the common engines (AMBER, GROMACS, etc), we’ll have a period of time when we release TWO force fields - one with vsites, one without.
RDKit ligand modification
PB – How are conformers generated for the simulation after the chemical change?
JW – It’s such a small chemical change (H → F) that we keep the coordinates the same and just minimize to clean it up.
Micelle
PB (DM to Jeff) – For your information: there is a raised issue within NMRLipids community about openff lipids (https://github.com/NMRLipids/Databank/issues/175). I might take a look at it quit soon in detail, but as for now this is maybe a good community/repository to track/evaluate lipid ff
RNA
PB – Is it possible to change the coordinates of the structure in the interchange? A potential use case is that you might have multiple monomers of the same NA and want to move it around.
JW – Traffic light system?
NCAA
PB – In priciple, does NAGL have guards against cases where it will behave poorly?
JM – It’s hard to guard for these cases it in general. There are limited guards in NAGL but they can’t be considered to be super safe.
PB – So the whole protein uses ff14sb parameters, and the dye uses sage?
JM – The dye residue has some ff14sb parameters because of the backbone similarity.
Zoom chat
05:00:43 From Jeffrey Wagner to Everyone:
The materials for today’s workshop can be found here: https://docs.openforcefield.org/en/latest/workshops/2024/vignettes.html
05:11:29 From Cesar to Everyone:
can you explain again what is interchange please?
05:12:33 From Cesar to Everyone:
Perfect thanks
05:25:13 From Cesar to Everyone:
I fouy can at some point, could explain a bit more how active sites can be used in applications. Apologies, for me it is a new concept
05:29:26 From Jeffrey Wagner to Everyone:
Virtual sites are a way to more accurately model the non bonded forces in a simulation. For example, some atoms have uneven charge distributions and aren’t well modeled by having just a point charge at their center, so taking some of the charge off their nucleus and putting it a short distance away can make a simulation more accurate.
05:36:08 From Cesar to Everyone:
Reacted to "Virtual sites are ..." with 👍
05:41:34 From Matt Thompson to Everyone:
(QCArchive is normally one of the more stable tools we interact with - we shove millions of molecules through it a year and only rarely have issues pulling them back down)
05:44:02 From Jeffrey Wagner to Everyone:
Reacted to "(QCArchive is normal..." with 🔥
05:44:59 From Matt Thompson to Everyone:
Reacted to "(QCArchive is normal..." with 🔥
05:45:01 From Matt Thompson to Everyone:
Removed a 🔥 reaction from "(QCArchive is normal..."
05:52:38 From pbuslaev to Jeffrey Wagner(Direct Message):
For your information: there is a raised issue within NMRLipids community about openff lipids (https://github.com/NMRLipids/Databank/issues/175). I might take a look at it quit soon in detail, but as for now this is maybe a good community/repository to track/evaluate lipid ff
05:54:06 From Jeffrey Wagner to pbuslaev(Direct Message):
Wow - This is awesome. I’ll share this with the team!
05:54:20 From pbuslaev to Jeffrey Wagner(Direct Message):
Reacted to "Wow - This is awesom..." with 👍
05:55:03 From pbuslaev to Jeffrey Wagner(Direct Message):
I can share additional details if need, so just let me know
05:56:47 From Jeffrey Wagner to pbuslaev(Direct Message):
I’m not super aware of the details, but our science lead, Lily, had done some poking around with lipid validation. Do you mind if she contacts you later if she has questions?
05:58:25 From pbuslaev to Jeffrey Wagner(Direct Message):
Yes, sure. That's fine. Do you need my contacts?
06:00:43 From Jeffrey Wagner to pbuslaev(Direct Message):
Yes please. Are you on our slack/want to be added?
06:01:34 From Jeffrey Wagner to pbuslaev(Direct Message):
(In either case, I’d love to have your email)
06:02:53 From pbuslaev to Jeffrey Wagner(Direct Message):
I guess I am not on your slack but can be useful to be added. Thanks. I guess personal email would be better for this: pbuslaev@gmail.com
06:03:54 From Jeffrey Wagner to pbuslaev(Direct Message):
Great, invite sent.
06:04:05 From pbuslaev to Jeffrey Wagner(Direct Message):
Thanks! Received
06:10:51 From Vaclav Hanzl to Everyone:
Many thanks Josh and Jeffrey! (Have to leave now unfortunately.)
06:11:57 From Cesar to Everyone:
is openFF able to handle cofactors? ATP, NADPH< FAD etc
06:13:11 From Cesar to Everyone:
ok, Thanks
06:18:49 From Matt Thompson to Everyone:
This bug was fixed yesterday, just not in a release yet 🙂
06:19:17 From Jeffrey Wagner to Everyone:
Reacted to "This bug was fixed y..." with 👍
06:29:18 From Matt Thompson to Everyone:
Star Trek hour 😎
06:38:02 From Cesar to Everyone:
very inetresting. Shall we able to expor those charges?
06:38:51 From Cesar to Everyone:
yes
06:49:11 From Jeffrey Wagner to Everyone:
To add on to what Josh said about “NAGL is not an AM1BCC charge assignment method” - this is the current state. Our goal in the coming months is to release a NAGL model that we do endorse for AM1BCC charge assignment, and when that happens, calling offmol.assign_partial_charges(“am1bcc”) will use NAGL when it’s available.
Debrief
JM –
Felt a little more chaotic/pacing was trickier to hold. If we do vignettes again we should focus more on showing what we can do rather than discussing how it all works. I think I covered things well and JW filled in when I missed important details. I think I was most familiar with the notebooks I wrote and less with the ones contributes by JW and MT. Also, if we do this again, we could say that the first hour is more basic stuff and the second hour is more advanced, and so folks might drop in at halftime.
MT –
Thought it went great. Was half-paying attention and doing other stuff. Most of my ideas for improvement were about “it’d be great if this was green/the tools were out”. I think the pacing was good for an audience of people that don’t work here.
JW –
Congrats on finishing up the live demos. This year was a big improvement on last year.
I forgot to do the #general channel announcement before this one, might be the reason for the low initial turnout 🤦♂️
The colab env failed on the QCSubmit example because it was broken by OpenEye vs. qcportal/the zstandard thing. I think this issue is more severe than I’ve previously assumed. If we caught this earlier we could have just kept OE from being installed on colab in the first place.
JM – Yeah, worth noting that colab is a HUGE pain to use for this.
JW – Yes, but it’s also a HUGE win that people can use our whole stack so easily in just a few minutes. Let’s not forget how much of a selling point this is to make attendees believe that our stuff is usable.
JM – Possible future self-running WASM notebooks in a few years.
Awesome back-and-forth with PB
Pacing seemed a little… rambling? Discussion of lots of good details but also some less important ones. Sometimes I could see things that we could start pre-executing but instead we talked a lot about the previous cell and then had nothing to say while the next one ran. I probably didn’t help by taking away rehearsal time by asking you to spend time on RNA+lipids at the 11th hour.
JM – If we do this again, we should reduce the scope/number of bignettes.
JM+JW – Maybe some rethinking of how notebooks are transitioned/introduced. Sometimes the audience wouldn’t know at a high level what we were about to see, but they’d hear a few minutes of caveats. So more context at the introduction about what we’re doing and why it’s hard to do in other ecosystems would be good.
2024_04_17 Protein prep Workshop
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