Mathieu Linares

You can now define some default coloring per element in VIAMD. On top of it, you can choose a specific atom-type coloring. Also works for @veloxchem.bsky.social files. #compchem

#compchem colleagues,

Want to learn about @veloxchem.bsky.social and @viamd.bsky.social?

Join us at The eChem workshop "Quantum Chemistry with Jupyter Notebooks", will take place in Marseille (France) from May 18th to May 22nd, 2026.

Information & registration:
echemarseille26.sciencesconf.org

So?

Have a jiggly weekend! #compchem

16th Edition of the European Symposium on Computing pi-Conjugated Compounds (CPiC), organized by Silvio Osella, CeNT, Univ. of Warsaw cpic16.cent.uw.edu.pl
#CompChemSky

Thanks again, Silvio, for the great organization!

Theor. Chem. Acc. (a @springer.springernature.com journal) sponsors the poster session of the 16th edition of the European Symposium on Computing Conjugated Compounds, greatly organized by Silvio Osella and taking place in Warsaw during these days. Thank you for hosting us!

#theochem #compchem

User interface of the CrystalNets web app

Architecture of the CrystalNets web app, showing client-side and server-side tasks.

“CrystalNets: a web app for topology determination of crystalline structures” — our latest preprint on @chemrxiv.org doi.org/10.26434/che...

Looking forward to the flat earth model. 🤪

Kamoulox !

🤝 Our collaboration with other leading EU #HPC Centres of Excellence has resulted a white paper providing guidance and best practices for CoEs aiming to build their #innovation and #commercialisation capabilities

Read more: bioexcel.eu/k7b9
DOI: dx.doi.org/10.13140/RG....

VeloxChem Quantum–Classical Interoperability for Modeling of Complex Molecular Systems Being a program written primarily in Python that strictly adheres to modern object-oriented software engineering and parallel programming practices, VeloxChem is shown to be suitable for the development of (semi)automatized workflows that extend its scope from first-principles quantum chemical purism to hybrid quantum–classical interoperability and some degree of semiempiricism. Methods are presented for building complex systems such as metal–organic frameworks, constructing molecular mechanics and interpolation mechanics force fields, conformer searches, system solvation, determining free energies of solvation, and determining free energy profiles of reaction pathways using the empirical valence bond method. The implementations are made intuitive with opportunities for interactive plotting and 3D molecular structure illustrations through the use of Jupyter notebooks.

Check out our latest paper! #compchem You will find descriptions and short examples of how VeloxChem integrates quantum chemistry with classical methods.
doi.org/10.1021/acs....

#compchem You can use viamd to read and analyze @veloxchem.bsky.social output file. You can read more about it following this link: github.com/scanberg/via...

C'est le problème des pauvres, ils sont pas suffisamment disrupteur pour trouver des solutions contre le changement climatique.

You can now save Ultra HD (8k) resolution screenshot in VIAMD, with or without the GUI. Here illustrated on a visualization of a Moebius ring calculated with @veloxchem.bsky.social. #compchem

Come and visit us at the @veloxchem.bsky.social booth at #watoc #compchem.

Road trip to #watoc! See you there. #compchem

Hi Jean-Philip. Long time no see. Pass by the @veloxchem.bsky.social booth if you have time.

On my way to the World Association of Theoretical and Computational Chemists (WATOC) meeting in Olso.

#WATOC #CompChemSky #ChemSky

www.watoc2025.no

I am sorry but the otter is the goat skogsduva.

See you there. I'll be at the @veloxchem.bsky.social booth. Presenting our QM software as well as @viamd.bsky.social. #WATOC #compchem

Signez la pétition Sauvons le Palais de la découverte

Pour la réouverture du palais de la découverte ! chng.it/gncnBRZnTc

Frontiers | Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software wh...

www.frontiersin.org/journals/bio...

Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations The bacterial mechanosensitive channel, MscL, opens in response to elevated membrane tension during osmotic shock. Some mutations, like L17A and V21A, can reduce the activation tension threshold, thus...

MscL channel opens up asymmetrically! Check out our latest story, spearheaded by my brilliant postdoc Olga

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

Happy #pride month! We believe that chemistry is for everyone. In the face of opposition that threatens the progress we've made, it's never been more important for us to promote equality of opportunities and make chemistry as open, inclusive and diverse as it should be: buff.ly/1dShs0l #ChemSky

See you there. I will be at the @veloxchem.bsky.social booth.

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

Get inside a bacterial cell with this cool combination of @cg-martini.bsky.social and @viamd.bsky.social

Also check out our recent webinars on each:

🎬 Whole cell simulation with Martini ▶️ youtu.be/fvFaPgSoM90

🎬 Visual analysis of #moleculardynamics with VIAMD ▶️ youtu.be/wVENzcx0XmQ

PolyPal: A Python Package for Molecular Dynamics Simulation of Amorphous Polymers Easily tunable and processable, porous organic polymers (POPs) have found increasing utility in various applications. Molecular modeling and simulations are invaluable tools in polymer science but remain under-reported in the POP literature. Accurate modeling and simulation of these materials could boost the discovery of high-performance POPs and allow for a more thorough contribution to big data. These polymers contain free volume-promoting structural units, such as iptycenes, and exhibit high glass-transition temperatures, excellent thermal stability, and tunable functionality. However, popular transferable force fields utilized in all-atomistic molecular dynamics (MD) simulations are not fully parametrized for intrinsically porous thermoplastic materials. We present a streamlined workflow for all-atomistic MD simulations of nonporous and porous amorphous polymer materials. In conjunction with the programs ORCA, Q-Force, Assemble!, and GROMACS, a highly accessible methodology is established for force field (FF) parametrization, creation of initial configurations, and simulation of various nonporous and porous polymers. This protocol can reproduce experimental bulk densities and fractional free volume values for amorphous polymeric materials with excellent accuracy and has been made available as a Python package, called PolyPal. As an example, we present our results using PolyPal on a series of nonporous and porous polymers that were previously synthesized and experimentally characterized. FF accuracy was also validated through solid-state NMR studies. These simulations will not only open new avenues for the rational design of high-performance POPs through the contribution of improved insight but also provide a streamlined pathway for simulating previously unexplored porous polymeric materials.

Very interesting #compchem article: pubs.acs.org/doi/10.1021/...

The Q-AMOEBA (CF) Polarizable Potential We present Q-AMOEBA (CF), an enhanced version of the Q-AMOEBA polarizable model that integrates a geometry-dependent charge flux (CF) term while designed for an explicit treatment of nuclear quantum e...

#compchem New paper in J. Phys. Chem. Lett.
: "The Q-AMOEBA (CF) Polarizable Potential".
Enhanced version of the Q-AMOEBA polarizable model integrating a geometry-dependent charge flux term while designed for an explicit treatment of nuclear quantum effects.
pubs.acs.org/doi/10.1021/...