Eliane Briand

This uses a nice trust region-style optimization to avoid resimulating for every Ɛ change in FF parameters. The fast convergenge shows the parameters space is less irregular than I thought it could be.

📜 New preprint! We developed PoGö, an algorithm to optimize the essential dynamics of GöMartini proteins based on all-atom simulations: www.biorxiv.org/content/10.1...

First slide for a "Why we do not use Kokkos" deck, from Sandia Lab (famously, maker of Kokkos)

what's the blessed way to use trilinos in a project without the "kokkos_launch_compiler" & other wrapper messing with the compilation of .cu in CMake? (not just a rant, plz link blog or example projects where that works)

[😅 unrelated pic 😅]

Les marchés publics de voyagistes - Contributions - 2025 - Aidez-nous à enrichir notre programme de travail - Plateforme de participation de la Cour des Comptes Corps de la contributionLes administrations et opérateurs publics, notamment ceux de l'enseignement supérieur et de la recherche, font appel à des agences de voyage (FCM, TravelPlanet…) pour l'hôtelle...

Vous pouvez soutenir ma proposition à la Cour des Comptes d'examiner les marchés publics de voyagistes, notamment dans l'enseignement supérieur et la recherche :
participationcitoyenne.ccomptes.fr/processes/co...

#esr #TeamESR #HelpESR

Helmut Grubmüller

📢 We are hiring #PhD students and #Postdocs at the
@mpi-nat.bsky.social in
in the Department of Theoretical and Computational #Biophysics in Göttingen 🇩🇪! 🔗 check our current job adverts at www.mpinat.mpg.de/grubmueller and find your project. Submit your #application today! #job

YouTube video by Curt Jaimungal Infinity Categories Explained for Undergrads | Emily Riehl

First 40mins is great lobbying for the category theory/HoTT industrial complex, increased my motivation to get into it

(Rest still a quality lecture by the interviewee - in an "intellectual tourism" sort of way, for me)

Come to my talk on ACS Fall 2025 about K+ channel ECC force field on 19 Aug😏

We also have our new developed GCMC FEP with benchmark.😉

#acsfall2025

"Get ready to learn chinese buddy"-type meme, except, it's NVidia CUTLASS not Chinese

thesis: LLM useful but not trillion-dollar-CAPEX useful

prediction: ✨🔮 i see... a lot of cheapo H100 in your future... 🔮✨

suggested pivot: forcibly jamming the ozaki scheme into whatever im doing

(mind you, this is already log likelihood, but the summing pattern across datapoints when far from the maximum gets pretty nasty)

CUDA code for a similar kind of extended precision summing code, here a fast2sum based cascading scheme. This takes a cascading level as template argument, with 1 being normal double, 2 using two double, one for running sum, another for the tally of the errors, and 3 and beyond holding the errors of the error sums of the level before.

as well as this, allowing the nifty fp192* format

*: conditions apply

C/C++ source code for a Kahan sum accumulator using __float 128 data type, the fabled quadmath floating point type. Kahan sum allows the additions of floating point number using two elements, one for the running sum, one for the running floating point addition error, providing an extended precision way of summing large arrays of disparate numbers, here almost equal to an "octuple" precision floating point number

today is the day i get to bring out this bad boy:

Graph showing the number of deposited experimental structure on the PDB. It is steadily rising without clear discontinuity since 2020-2021.

Graph showing the number of released X-ray crystallography structure on the PDB. It is steadily rising without clear discontinuity since 2020-2021.

<implied hot take about alphafold "solving" the protein structure problem>

i think it's fine, application-specific pre/post-processing are convenient; and for more complex models, it could very well be faster for prototyping ("real" programming language vs DSL where you forcefit what you want to do in an existing construct). might drop a Stan version when finished, though

slowly realizing i'm afflicted by the curse (rewriting Stan, but less general)

Le Monde reporting that a French scientist traveling to Houston to attend a conference was denied entry to US after a search of his phone & computer revealed messages critical of Trump's science cuts, "which [says CPB] conveyed hatred of Trump & could be qualified as terrorism". Computer confiscated

you know you're overperforming when the audience is pulling up your google scholar /during/ the talk #Hünfeld2025 (session 1)

if VMD is so good, why isn't there a VMD 2... wait...

(Joke aside, constant pH MD and protonation coupling talk tomorrow, excited!)

Being the #Hünfeld2025 event photographer means I can't escape. Being a presenter means you can't either --- so let's connect there!

And a documentation website, too

grubmueller.pages.mpcdf.de/docs-gromacs...

Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes. Conversely, conformational and environmental changes of the biomolecule affect the protonation state of these groups. With few exceptions, conventional force field-based molecular dynamics (MD) simulations neither account for these effects nor do they allow for coupling to a pH buffer. Here, we present design decisions and applications of a rigorous Hamiltonian interpolation λ-dynamics constant pH method in GROMACS, which rests on GPU-accelerated Fast Multipole Method (FMM) electrostatics. Our implementation supports both CHARMM36m and Amber99sb*-ILDN force fields and is largely automated to enable seamless switching from regular MD to constant pH MD, involving minimal changes to the input files. Here, the first of two companion papers describes the underlying constant pH protocol and sample applications to several prototypical benchmark systems such as cardiotoxin V, lysozyme, and staphylococcal nuclease. Enhanced convergence is achieved through a new dynamic barrier height optimization method, and high pKa accuracy is demonstrated. We use Functional Mode Analysis (FMA) and Mutual Information (MI) to explore the complex intra- and intermolecular couplings between the protonation states of titratable groups as well as those between protonation states and conformational dynamics. We identify striking conformation-dependent pKa variations and unexpected inter-residue couplings. Conformation–protonation coupling is identified as a primary cause of the slow protonation convergence notorious to constant pH simulations involving multiple titratable groups, suggesting enhanced sampling methods to accelerate convergence.

Constant pH with FMM characteristics, now out!

pubs.acs.org/doi/10.1021/...

3d render of a ceramic cup full of very much not to scale water molecule (space filling sphere), nearby a protein in ribbon representation, over a science paper as table.

cup of TIP3P