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Xin@QuantumChem @xinquantum.bsky.social · Aug 13

I'd like to name it as "QM/MM".

Xin@QuantumChem @xinquantum.bsky.social · Aug 6

playground.tracto.ai/playground/n...

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playground.tracto.ai

Xin@QuantumChem @xinquantum.bsky.social · Aug 1

This old theory is revitalized by deep learning. Building accurate kinetic energy functionals (< 0.5 kcal/mol) may be harder than climbing to the top of exchange-correlation Jacob's ladder.🪜

IOPP Machine Learning and AI @iopp-mlresearch.bsky.social · Aug 1

#MachineLearning (ML) for orbital-free density functional theory (OF-DFT) and OF-DFT for ML. Manzhos and coworkers tackle the kinetic energy functional in this new #MachineLearningScienceandTechnology article. #compchem #CompChemSky Read it here: bit.ly/45eGM0f

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Xin@QuantumChem @xinquantum.bsky.social · Jul 27

Cunning ChatGPT bypassing 3D depth analysis, and calling the rdkit function to generate the coordinate of an Ibuprofen. Grok3 just failed this test and misrecognized it as glucose, as expected.

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Xin@QuantumChem @xinquantum.bsky.social · Jul 23

Boltz2 can be run on a $430 RTX5060 Ti (16G) card, although it's much slower than ~$30,000 H100 (RTX 5060 Ti: 1min 47s, H100: 18s), but it doesn't matter, because the cold-start time is about 1 minute for both cards.
#CompChemSky #CompChem #GPU

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Xin@QuantumChem @xinquantum.bsky.social · Jul 14

Kvass and Khinkali

Xin@QuantumChem @xinquantum.bsky.social · Jul 12

This is a transition state structure (red is oxygen, blue is Nitrogen, Green is Nicle) of C-N splitting reaction. Create a deamon around the structure breaking the C-N bond.

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Xin@QuantumChem @xinquantum.bsky.social · Jul 12

This is creepy, but lots of fun. Gemini Veo has a perception of spatial depth and can rotate the molecules.
Inspired by www.youtube.com/watch?v=mDyt...
#compchem #compchemsky

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Xin@QuantumChem @xinquantum.bsky.social · Jul 11

It should be the warm start. AIMNet2's model downloading and loading are also fast.

t0 = perf_counter()
E=mol.get_total_energy()
t1 = perf_counter()

Xin@QuantumChem @xinquantum.bsky.social · Jul 9

Correctness: AIMnet2 should be AIMNet2. Single-point energy calculation.

Xin@QuantumChem @xinquantum.bsky.social · Jul 9

Just run the following command in Colab. Works fine!
!uv pip install --system git+https://github.com/aligfellow/vib_analysis.git

Xin@QuantumChem @xinquantum.bsky.social · Jul 9

I ran a benchmark on a protein with ~3450 atoms. AIMnet2 takes 4.6 seconds, and UMA(small) takes 7.9 seconds. CUDA 12.4 on a Tesla T4. Additionally, the AIMnet2 checkpoint file is only 11.1 MB. The testing notebook link is shared.
#compchemsky #compchem

colab.research.google.com/drive/1g1PiW...

Google Colab

colab.research.google.com

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Xin@QuantumChem @xinquantum.bsky.social · Jul 5

This is a very interesting package. I will try this on colab notebook.

Ali Goodfellow @aligoodfellow.bsky.social · Jul 3

Wrote a bit of code to quickly analyse vibrational modes from QM calculations! #compchem
github.com/aligfellow/v...
Returns a list of internal coordinates associated with the vibrational mode, can be used from command line on xyz trjfiles or orca or gaussian outputs etc.

GitHub - aligfellow/vib_analysis: Quick analysis of xyz vibrational mode trajectory

Quick analysis of xyz vibrational mode trajectory. Contribute to aligfellow/vib_analysis development by creating an account on GitHub.

github.com

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Xin@QuantumChem @xinquantum.bsky.social · Jul 4

UMA (uma-sm) combined with NEB successfully locates the transition state and path for a Ni-catalyzed reaction. UMA prediction lies between two DFT functional, and the transition state closely matches the result from a literature: www.nature.com/articles/nat...

#compchemsky #chemsky #compchem

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Xin@QuantumChem @xinquantum.bsky.social · Jun 27

The relationship between Ki and IC₅₀ is described by the Cheng–Prusoff equation. And William L. Jorgensen et al. did an effective calculation for predicting potency in his paper during pandemic.
pubs.acs.org/doi/10.1021/...

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Xin@QuantumChem @xinquantum.bsky.social · Jun 26

Guess the name？
#Cocktail #Liquor #Alcohol #cursor

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Xin@QuantumChem @xinquantum.bsky.social · Jun 16

That's a nice update! Thanks

1

Reposted by Xin@QuantumChem

Jan @dermewes.bsky.social · Jun 14

2nd virtual lecture in the DFT&Application series starts today at 1500hrs CET (in 15 minutes!). Topics are Hartree Fock, SCF, and their connection to DFT.

Join us in Zoom: us06web.zoom.us/j/8607128794...

#compchem #dft

Join our Cloud HD Video Meeting

Zoom is the leader in modern enterprise cloud communications.

us06web.zoom.us

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Reposted by Xin@QuantumChem

Jo Ma @myzzzz.bsky.social · Jun 11

Hey Jan, I just completed UMA benchmark tests on large molecules (biomolecules, macrocycles, and more): quantabricks.substack.com/p/uma-testin... In short, when atoms number below 700, uma is more expensive. Otherwise, GFN2-xTB is more expensive
#compchem #CompChemSky

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Xin@QuantumChem @xinquantum.bsky.social · Jun 12

An interesting opportunity to help the horseshoe crab (more closely related to spiders). gothamist.com/news/new-yor...

New York beaches are dating hot spots for horseshoe crabs

Beneath a full moon in Jamaica Bay, horseshoe crab love was in the air.

gothamist.com

Xin@QuantumChem @xinquantum.bsky.social · Jun 5

Short answer: UMA is more time-consuming than xTB on a single CPU core (AMD EPYC 7401P). For a single-point calculation of semaglutide (582 atoms), UMA took 76.36s, while xTB took 29.42s.
@myzzzz.bsky.social Could you please do more tests and share a report show the scaling or parallel speedup.

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Xin@QuantumChem @xinquantum.bsky.social · Jun 4

Surprisingly, the UMA (by meta) model captures the bond-breaking process in the carbon nanotube stretching test, similar to GFN2-xTB. I hadn't expected deep learning models to extrapolate over bond lengths.
#compchemsky #chemsky

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Xin@QuantumChem @xinquantum.bsky.social · May 27

It's a great time to participate in the horseshoe crab protection activity (helped with counting and tagging). I had only heard stories about the blue blood legend in evolution before, but this time I saw it with my own eyes.

#aquatic #science #NYC #drug

Xin@QuantumChem @xinquantum.bsky.social · May 22

JupyterNotebook: github.com/myzzzz6/AI4C...

Xin@QuantumChem @xinquantum.bsky.social · May 22

Get Started with Meta’s Molecular AI Model UMA on Google Colab
open.substack.com/pub/quantabr...

Get Started with Meta’s Molecular AI Model UMA on Google Colab

Meta and collaborators released the molecular foundation model UMA (Universal Model for Atoms) and its training dataset OMol25 (at ωB97M-V/def2-TZVPD level) this month.

open.substack.com