🔬 Visual Interactive Analysis of Molecular Dynamics (VIAMD)

VIAMD is an interactive analysis tool for molecular dynamics (MD), developed in C/C++. Created through a collaboration between LIU (Norrköping) and the PDC Center for High Performance Computing (KTH, Stockholm), it provides a noscriptable interface for defining operations over trajectory frames.

🧠 With VIAMD, you can:

Interactively analyze MD simulations

Use a simple noscript language to define frame-based operations

Visualize results across multiple application windows

🔗 Get the code:
https://github.com/scanberg/viamd

🎓 Learn how to use it:
https://www.youtube.com/playlist?list=PLNx9MpJY8ffr9CeK7WefdOnuGRw_E5rSj

📄 Read the publication:
https://pubs.acs.org/doi/10.1021/acs.jcim.3c01033

🧪 Microsoft Quantum – Applied Scientist in Drug Discovery (Contract Position)

The Microsoft Quantum team is hiring an Applied Scientist to work at the intersection of Machine Learning and Drug Discovery.

📍 Remote | ⏳ 18-month contract

Responsibilities: • Design and develop advanced ML models for drug discovery.
• Produce high-quality, maintainable, and well-documented code.
• Analyze research data to generate insights.
• Collaborate with interdisciplinary teams and customers.

Requirements: • Ph.D. or equivalent experience in Computational Biology, Bioinformatics, Machine Learning, or related fields.
• Proven research experience in drug discovery.
• Strong coding and ML model development skills.
• Background in computational biology.
• Excellent problem-solving, communication, and teamwork skills.

Soft Skills: • Strong troubleshooting and organizational skills.
• Excellent documentation habits.
• Passion for ML's transformative role in healthcare.
• Adaptability to new technologies.

📧 Apply by sending your CV to:
contract-roles-aicms@microsoft.com
(Subject: Applied Scientist in Drug Discovery)

🔗 More details:
https://psi-k.net/jobs/microsoft-quantum-applied-scientist-in-drug-discovery-contract-position/

🛑 No deadline specified — apply as soon as possible.

Also, the new paper describing ORCA 6 is out. Remember to always support your software development by citing the related papers. 👇

🔬 AmberTools25 Released 🔬

On behalf of the entire Amber development team, we’re pleased to announce the release of AmberTools25, a suite of programs supporting biomolecular simulations.

📌 Visit: https://ambermd.org
Check the "AmberTools25" and "Download Amber" tabs for details.

🛠 What’s new in distribution:
Amber (which includes pmemd and other tools) is updated only in even-numbered years. However, Amber24 is now packaged as a stand-alone tarball, which can be built independently of AmberTools — simplifying installation on HPC systems.

➡️ If you already have Amber24, no need to reinstall.
➡️ New users or those installing on a new cluster: download the new tarball.

🙏 Special thanks to the developers who led AmberTools25 testing — you know who you are.
🧪 Of course, we can’t test on every platform, so please report issues via the Amber mailing list.

🐍 Conda users: the Conda installation remains a convenient option. More info is available under the "Download Amber" tab.

🚀 GROMACS 2025 Released!

🔹 New Features:
• PLUMED (feature-limited) now usable without patches on non-Windows builds
• Basic support for Neural Network Potentials (NNP) trained with PyTorch
• Improved OpenMP parallelization for pair search and domain decomposition — better GPU performance
• AMD HIP now supported as GPU backend (limited to NBNxM kernels)
• Expanded ensemble equilibration now continues across simulations via .mdp options
• GPU-direct communication enabled by default when supported by MPI
• NVSHMEM-based GPU communication for PP halo exchange boosts multi-GPU scaling

📚 Read the Docs: https://manual.gromacs.org/2025.1/index.html
📝 Release Notes: https://manual.gromacs.org/2025.1/release-notes/index.html
💾 Download: https://manual.gromacs.org/2025.1/download.html

Meet El Agente, an autonomous AI for performing computational chemistry

By minimizing the technical barriers traditionally associated with computational chemistry, El Agente is a step toward more inclusive, accessible, and scalable scientific research worldwide.

https://acceleration.utoronto.ca/news/meet-el-agente-an-autonomous-ai-for-performing-computational-chemistry

📢 Online Conference: "From Theory to Application"
📅 Dates: 24–26 June 2025
🌐 Format: Webinar (online, free participation)

The Organizing Committee warmly invites researchers, students, and professionals from academia and industry to join the first edition of the conference "From Theory to Application: Wrocław Meetings on Computational and Experimental Sciences", organized by the Faculty of Chemistry, University of Wrocław.

The event will feature lectures, poster sessions, and flash presentations (special sessions for young researchers). We encourage poster submissions at the time of registration.

Topics covered include:

🔹 Computational approaches in drug design
🔹 Electronic structure and compound design with specific physicochemical properties
🔹 Relationship between chemical structure and practical applications
🔹 Magnetic properties and their everyday applications
🔹 Artificial Intelligence applications in material science and biologically active compounds
🔹 Modern methods for macro-system modeling
🔹 Designing modern materials via in silico methods

🔗 Details and registration: makromol.uwr.edu.pl/en