NVIDIA Deep Learning Institute (DLI) is conducting a series of free virtual workshops for academia and higher education in the North America. Join the MolSSI Industrial Training Program and our Software Scientist and Certified Instructor, Dr. Sina Mostafanejad for a hands-on Fundamentals of Accelerated Computing with CUDA C/C++ workshop on November 10 from 11:00AM-7:00 PM ET (8:00AM- 4:00PM PST)

• Register here.

You can stay up-to-date about the upcoming workshops by subscribing to our newsletter here.

The Molecular Sciences Software Institute (MolSSI) and Intel invite you to attend our hands-on Basics of Accelerated Computing with Intel OpenMP GPU Offload virtual workshop on Oct. 27, 2023 from 11:30 – 16:00 ET. Come join us and see how Intel OpenMP helped community codes like NWChem perform compute- and data-intensive tasks more efficiently. 

• Date and Time: Oct. 27, 2023 from 11:30 – 16:00 ET
• Registration link (closed)
• Recording link

You can stay up-to-date about the upcoming workshops by subscribing to our newsletter here or following the updates posted on our Industrial Training Program webpage.

The Molecular Sciences Software Institute is now accepting proposals for its 2024 Software Workshops. Proposed events should focus on software-related challenges relevant to the broad field of computational molecular sciences, including biomolecular and macromolecular simulation, quantum chemistry, and materials science. MolSSI workshops typically last 2-3 days and receive logistical and financial support from the Institute. Workshops may be held at locations convenient to the target audience, or we can provide assistance in identifying a venue or host the workshop at our headquarters in Blacksburg, Virginia.

We encourage participation from a diverse audience and representatives from academic institutions, industry, national laboratories, and the cyberinfrastructure community. MolSSI Software Workshop proposals will be reviewed promptly by the MolSSI Board of Directors using selection criteria based on (1) the relevance of the proposed workshop topic to the Institute’s goals; (2) the breadth of the impact across the molecular sciences; and (3) the strength and diversity of the participant list.

Proposal Requirements:

A complete MolSSI Software Workshop Proposal must include:

• A workshop description, including motivation and relevance to the computational molecular sciences (maximum of two pages);
• A list of potential speakers and participants that is broadly inclusive;
• A proposed venue and anticipated budget.

The deadline for submitting your proposal is February 1st, 2024. 

Tuesday, Sept. 12, 2023
Release Information and Documentation: https://molssi.github.io/QCFractal/

The Molecular Sciences Software Institute is excited to announce the release of QCArchive v0.50. QCArchive is a MolSSI open-source software product that allows users to run a large number of QM calculations and archive the results. This release has numerous new improvements and features:

• Enhanced, more consistent interface
• Better performance for dataset operations
• More calculation types
• New dataset management features
• Improved server performance

Want to learn more about QCArchive and see how it could benefit your research team? Join us for a free online webinar on September 21.

Join us on Thursday, Sept. 21 from 1-3 pm ET (10 am – 12 pm PT) for a webinar introducing the newly released QCArchive software.  QCArchive is a MolSSI open-source software product that helps users run large numbers of QM calculations and archive the results.  In this interactive webinar, we will introduce the features, use cases, and fundamentals of QCArchive. Each participant will gain hands-on experience using QCArchive, so you can see how QCArchive could benefit your research team.  No prior experience with QCArchive is required; this workshop will start from the very beginning.  Register here.

Prerequisites: No prior experience using QCArchive is needed to participate in the webinar.  The interactive portion of the workshop will use Python, so basic understanding of Python syntax is recommended.  The level of Python knowledge required is very basic; completing the Introduction lesson of the MolSSI Python Scripting workshop would be sufficient. Information about installing the software using conda will be set out to all participants ahead of the workshop.  

Space is limited and preregistration is required!  Registration form

MolSSI Community Highlights spotlight exceptional examples of research and education enabled by MolSSI software and educational resources.

Dr. Jeffrey Wagner (Technical lead at the Open Force Field Consortium) and his team focus on the development of accurate and transferable molecular mechanics force fields using a combination of quantum mechanics (QM) and experimental data. In this post, Dr. Wagner tells us how MolSSI tools have played a role in advancing the development and validation of molecular forcefields.

MolSSI:

Hi Dr. Wagner, thank you for taking the time to chat with us! Your research area seems fascinating. Could you provide a brief introduction to your research area and share what your team is currently focusing on?

Dr. Wagner:

The Open Force Field Consortium (OpenFF) is a collaboration of academic and industrial researchers that aims to develop accurate and transferable molecular mechanics force fields using a combination of quantum mechanics (QM) and experimental data. The consortium’s ultimate goal is to enable more accurate computational simulations of molecular systems in a variety of fields, including drug discovery and materials science. 

To achieve this goal, we use a variety of computational and experimental techniques, including QM calculations, molecular dynamics simulations, and machine learning methods, to generate and validate force field parameters. We also work to develop best practices and standards for force field development, validation, and sharing.

MolSSI:

Can you share how MolSSI software tools or resources have been utilized to accomplish specific research objectives in your projects?

Dr. Wagner:

The Open Force Field Consortium (OpenFF) heavily relies on the MolSSI software tools and resources to achieve specific research goals. The Parsley and Sage force field lines, which are used in many of our research projects, were developed based on quantum chemical data calculated on the MolSSI QCArchive. This data serves as a reference to validate and improve our force fields. Furthermore, the OpenFF QCSubmit package and qca-dataset-submission pipeline interface with the MolSSI APIs to allow us to easily create cross-ecosystem workflows, making it possible to use the MolSSI ecosystem tools to fit and validate force fields that interact with the OpenMM and other toolkits. Many of our lead employees were trained in software development at MolSSI, which has greatly contributed to the development of the OpenFF toolkits.

We also make heavy use of the MolSSI QCArchive and general QC ecosystem to generate and share quantum chemical datasets for force field fitting. This includes using the QCSubmit package to automatically submit calculations to the QCArchive for small molecule and protein systems. The QCArchive provides us with access to a large database of computed molecular properties, which allows us to validate and benchmark our force fields against accurate reference data. In addition, many of our repositories, including the OpenFF toolkit, are based on the MolSSI project cookiecutter. Overall, the collaboration between OpenFF and MolSSI has been instrumental in our research endeavors, allowing us to develop more accurate and transferable force fields and to improve the accessibility and sharing of quantum chemical datasets.

MolSSI:

It’s great to see the impact of MolSSI resources on your work. Could you please share some of your significant findings or results facilitated by the MolSSI software tools or resources?

Dr. Wagner:

We have published several papers incorporating MolSSI software tools and resources, including the development and benchmarking of the Parsley and Sage small molecule force fields. 

MolSSI

MolSSI greatly values our collaboration with the Open Force Field Consortium. We extend our thanks to Dr. Wagner for sharing his insights with our community. We’re excited to continue supporting their important work in developing accurate molecular mechanics force fields.

Here are some publications that incorporate MolSSI software tools or resources from The Open Force Field Consortium:

• Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field: https://doi.org/10.26434/chemrxiv-2022-n2z1c 
• Collaborative assessment of molecular geometries and energies from the Open Force Field: https://doi.org/10.1021/acs.jcim.2c01185 
• Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale: https://doi.org/10.1021/acs.jcim.2c01153 
• Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field https://doi.org/10.1021/acs.jctc.1c00571 
• End-to-end differentiable construction of molecular mechanics force field https://doi.org/10.1039/D2SC02739A 
• Capturing non-local through-bond effects when fragmenting molecules for quantum chemical torsion scans https://doi.org/10.1101/2020.08.27.270934 
• Benchmark Assessment of Molecular Geometries and Energies from Small Molecule Force Fields https://doi.org/10.12688/f1000research.27141.1 
• Driving torsion scans with wavefront propagation https://doi.org/10.1063/5.0009232 

All of the Parsley and Sage force fields here: https://zenodo.org/record/7889050