RSE @ OMSF (biomol MD, free energy calcs, etc...), @MDAnalysis and @openfreeenergy core developer | he/him - views are my own
England, United Kingdom
Joined June 2009
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Irfan Alibay retweeted
Are you a new or prospective MDAnalysis user?
Join us for our online training workshop for a basic introduction to MDAnalysis and hands-on tutorials!
🗓️ October 25, 15:00 UTC
🔗 Apply by September 30: eventbrite.com/e/68163176796…
Irfan Alibay retweeted
The 2024 edition of the Free Energy Workshop will take place in Leiden, Netherlands, 13-15th May, 2024!
We have not yet opened registration, but you can already book the dates in your calendars.
Keep an eye on the wiki for further information: alchemistry.org/wiki/2024_Wo…
#alchemy2024
Awesome work by @mikehenry42, alongside his previous push for py3.11 we can finally unblock a lot of the downstream ecosystem!
Happy to announce @ambermdprog Ambertools 23 now has an osx-arm64 build on @condaforge 🚀
Now you can install ambertools without having to use Rosetta 2 emulation 🎉
Big thanks to @mwt_dev @jaime_rgp @ghutchis @hainm_comp @isuru_f for all of their help! 🙌
A few details 🧵
I should clarify, MM-(G/P)BSA have their place in a free energy estimation workflow. Indeed we've found the Nwat approach to be reasonably good at retrospective evaluations of fragment enumeration. BUT folks shouldn't ignore error bars in predictions.
Your error bars on multiple repeats are usually ~ 2-5 kcal/mol (at least they are for fragments). Anyone predicting on differences within that range... probably didn't do repeats.
Irfan Alibay retweeted
🔥off the Arxiv press: SILVR a generative diffusion model for molecule generation from X-ray fragment data: arxiv.org/abs/2304.10905
✅ Conditioning for X-ray fragments
✅ Linking and merging X-ray fragments
✅ Molecules fit in binding site
❌ No retraining needed
Irfan Alibay retweeted
My team is recruiting an organic chemistry postdoc at LANL. Feel free to contact me directly.
be reasonably easy to implement. We would definitely be happy to see such a contribution to the code base if folks find it useful.
Our guesser infrastructure is also in progress of being completely updated for the 3.0 release, which should make things easier [2/2]
By default we try not to guess for folks, there are several corner cases where that can go wrong, for example if you use HMR or if you have a coarse grained system. We do have a means to guess elements from types: docs.mdanalysis.org/1.1.1/do… and guessing from a mass dictionary [1/2]
Yes! Just use the `element` keyword. See docs.mdanalysis.org/stable/d… for more details.
Irfan Alibay retweeted
MDAnalysis will participate in #GSOC 2023! If you have some experience with #MD or other simulations at the molecular scale and if you like #coding to solve problems in #physics #chemistry #compchem #biochemistry #materialsscience is your thing: read mdanalysis.org/2023/02/22/gs…
ALT Google Summer of Code 2023 with MDAnalysis.
Link to the poster if you don't happen to be at #bps2023 github.com/IAlibay/MDAnalysi…
Please come by for a chat! I'll be there during breaks throughout the day too!
Last year, @MDAnlaysis released a whitepaper outlining our proposed "MDAKits" -> github.com/MDAnalysis/MDAKit…
For those at #bps2023, hear more at @HighSpeedMode's poster(B446) on MDA today
But first, let's take a quick walk through MDAKits+the idea behind them- with some cute cats!
We do have a contribution guide in our user documentation: userguide.mdanalysis.org/sta…
We always welcome any additions/comments/suggestions on how we can improve. Please do open up an issue: github.com/MDAnalysis/UserGu…
Irfan Alibay retweeted
Attending #BPS2023 and want to become the proud owner of a shiny new @mdanalysis sticker or fridge magnet? Come find me (look for the blue hair 😜 ), @HighSpeedMode, @lilyminium or @orbeckst !
