MolSSI Intro
The Molecular Sciences Software Institute
A nexus for science, education, and cooperation for the global computational molecular sciences community.
Software Infrastructure
Education Initiative
Industrial Training
Industrial Training
Software Fellowship Program
Community Workshops
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Education at the MolSSI

Education of students, post-docs, and faculty on programming and Best Practices in Software Development is a large part of MolSSI's mission. Our education program consists of our cohorts of Software Fellows, online training materials, and multiple workshops online and at various locations each year around the US.
Software Fellowships

Meet Our Fellows

The MolSSI continues to fund prestigious software fellowships that recognize advanced graduate students and postdocs pursuing the development of software infrastructure, middleware, and frameworks that will benefit the broader field of computational molecular sciences, including biomolecular and macromolecular simulation, quantum chemistry, and materials science.

The Molecular Sciences Software Institute (MolSSI) is pleased to announce that the 2023-24 Software Fellowship competition will be open for submissions for ONE-YEAR Fellowships (from 1 July 2023 thru 30 June 2024) on February 15. These prestigious Fellowships recognize advanced graduate students and postdocs pursuing the development of software infrastructure, middleware, and frameworks that will benefit the broader field of computational molecular sciences, including biomolecular and macromolecular simulation, quantum chemistry, and materials science. Recipients will have the opportunity to work with scientists at the MolSSI in order to implement recommended best practices, putting the Fellow’s project on a firm foundation. Fellows will receive specialized training in state-of-the-art software design principles and tools, and they will engage in outreach and educational efforts organized by the MolSSI.  Each Fellow will be assigned a mentor among the Institute’s Software Scientists, who will oversee their software development efforts and training.  In addition, the 2023-24 Fellows will spend a week at MolSSI HQ (typically in late July or August; Sunday PM through Friday PM) to interact with the Software Scientists during their “Software Best Practices Boot Camp.”

Inquiries to:

The MolSSI Software Fellowships will include a number of benefits:

Graduate Student Fellowships:

  • A generous stipend of $40k total for the 12-month Fellowships, plus tuition and required fees;
  • Travel allowances sufficient to fully cover visits to the MolSSI headquarters, as well as participation in MolSSI workshops or summer schools;
  • Access to MolSSI computational resources.

Postdoctoral Fellowships:

  • A generous stipend of $50k total for the 12-month Fellowship;
  • Travel allowances sufficient to fully cover visits to the MolSSI headquarters, as well as participation in MolSSI workshops or summer schools;
  • Access to MolSSI computational resources.

Note that MolSSI Fellowships are paid from NSF Participant Support funds. The only allowable expense categories are stipend, tuition and fees; F&A (indirect costs) and health insurance costs are not allowed.

Eligibility and Selection Criteria:

The MolSSI Software Fellowship program is presently limited to graduate students and postdoctoral associates at accredited U.S. academic institutions. Graduate student Fellows are expected to be enrolled full time at their home university, and postdocs must be fully employed or have an offer of full employment prior to acceptance of the award.  The MolSSI Software Fellowships are an equal opportunity program open to all qualified persons without regard to race, gender, religion, age, physical disability or national origin.  Awardees may accept other concurrent awards that do not require a significant time or service commitment.

MolSSI Software Fellows will be selected by the MolSSI Science and Software Advisory Board based on (1) the quality of the applicant’s software research proposal and its relevance to the Institute’s goals; (2) the applicant’s research productivity, including previous software-development efforts; (3) previous academic performance; and (4) external references.

Application Requirements:

A complete MolSSI Software Fellowship Application must include:

  • Project description (maximum of two pages, not including references);
  • Current curriculum vitae;
  • Undergraduate transcripts (graduate applicants only); graduate transcripts (all applicants);
  • Examples of previous software development products (e.g. links to source-code repositories or other code samples);
  • Two letters of support, one of which must come from the applicant’s current research adviser;

Please complete the application and upload the required documents HERE.
Letters of recommendation should be uploaded separately by your references HERE.

To receive full consideration for a Software Fellowship, all application materials (including letters of recommendation) must be submitted by April 1, 2023.

Additional Information:

  • Award Number (FAIN): 2136142
  • Award Instrument: Cooperative Agreement
  • Award Date: 07/30/2021
  • Award Period of Performance: Start Date: 08/01/2021 End Date:
  • Project Title: S2I2: Impl: The Molecular Sciences Software Institute
    Managing Division Abbreviation: CHE
  • Research and Development Award: Yes
  • Funding Opportunity: NSF 20-1 Proposal & Award Policies & Procedures
    Guide – PAPPG
  • CFDA Number and Name: 47.049 Mathematical and Physical Sciences

Pratyush Tiwary, University of Maryland, College Park
Cecilia Clementi, Free University Berlin
Teresa Head-Gordon, University of California, Berkeley

In recent years, the field of machine learning (ML) has seen an incredible and sustained surge in interest. From image classifiers to board games to protein structure prediction, ML and big data and internet are making large impacts in nearly every field, including chemistry and molecular sciences. In 2019 MolSSI organized a ML and chemistry workshop at which point perhaps one could have been skeptical about the impact of ML in chemistry. With the passage of three years, the likely number of ML skeptics in chemistry is much smaller. A lot more has happened since 2019 and there is an urgent need to assess where we are as a community, as well as establish the software needs and directives.

This workshop, which will be held from May 31 to June 2, 2023, at the University of Maryland, will look at the following questions/areas through invited talks from industry/academia experts, brainstorming sessions and poster sessions:

(a) How to implement public access to reliable benchmark data to enforce reproducibility.
(b) What software tools & infrastructures are missing for chemists to use ML in everyday work?
(c) How to train the next generation of chemistry students who can use such ML software.
(d) Open-source standards that need to be set and met, which can often be challenged by the intellectual property rights related to these novel and important approaches.
(e) Discussions on problems faced in general in Machine Learning for Chemistry.
(f) Machine Learning for Chemistry from an industry perspective

A limited number of students/postdoc/additional faculty will be accepted for participation in the workshop. Preference will be given to those presenting posters; if accepted, they will be provided partial reimbursement for travel and accommodation.

Please submit your registration request (deadline Feb 24, 2023) at this link. Should you have additional questions about content or other aspects of the workshop, contact Prof. Pratyush Tiwary at

List of invited speakers:

  1. Robert Abel, Schrodinger
  2. Rianne van den Berg, Microsoft Research
  3. Luigi Bonati, IIT Genoa
  4. Rose Cersonsky, UWMadison
  5. Bingqing Cheng, IST Austria
  6. John Chodera, MSKCC
  7. Kangway Chuang, Genentech
  8. Connor Coley, MIT
  9. Roberto Covino, Frankfurt Institute for Advanced Studies
  10. Elizabeth Decolvenaere, D. E. Shaw Research
  11. Andrew Ferguson, University of Chicago
  12. Rafael Gomez-Bombarelli, MIT
  13. Mojtaba Haghighatlari, Pfizer
  14. Oles Isayev, Carnegie Mellon University
  15. Shantenu Jha, Rutgers University
  16. Aditi Krishnapryin, UC Berkeley
  17. Rajat Maji, UCLA
  18. Adrian Roitberg, University of Florida
  19. Simon Olsson, Chalmers University of Technology
  20. Francesco Paesani, UCSD
  21. Guido Falk von Rudorff, University of Kassel
  22. Patrick Sahrmann, University of Chicago
  23. Sapna Sarupria, UMinnesota
  24. Mark Tuckerman, NYU
  25. Omar Valsson, University of North Texas
  26. Andrew White, University of Rochester

The Molecular Sciences Software Institute (MolSSI) and Intel invite you to register for the upcoming Fundamentals of Data-Parallel C++ and SYCL workshop:

We encourage everyone to sign up as early as possible due to the limited number of seats available.

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

After reviewing many impressive applications, the MolSSI is pleased to announce that the Science and Software Advisory Board has selected our new 2022-23 Software Fellows! They are:

  • Melisa Alkan, Iowa State University
  • Samuel Bekoe, University of California, Irvine
  • Maria A. Castellanos, Massachusetts Institute of Technology
  • Pratiksha Gaikwad, University of Florida
  • Alexander Heide, University of Georgia
  • Jiyoung Lee, University of Texas at Austin
  • Mary Pitman, University of California, Irvine
  • Thais Scott, University of California, Irvine
  • Kirill Shmilovich, University of Chicago
  • Xiao Wang, Purdue University
  • Zachary Windom, University of Florida

Our new MolSSI Software Fellows will receive a full year of support and mentoring by the MolSSI’s Software Scientist team.

The many exceptional applicants made the selection process extremely difficult. We are confident that our new Fellows will use this opportunity to excel in their research areas, and grow as researchers & scientists in their individual fields.

Congratulations to all our new fellows; we’re incredibly excited to have you on board!

MolSSI’s Materials Science Workshop, organized by Prof. Dominika Zgid at the University of Michigan, is intended to connect the materials science community and to identify and examine the specific initiatives that MolSSI can undertake that will be most beneficial. While the materials science community is very large and diverse, we will focus here on the part of the community where extensive interactions with the theoretical chemistry community are already either established or desired in the future. We will also have extensive discussions on how to “cast” our net wider and connect with other parts of this community.

This workshop will have two parts:

  1. The VIRTUAL portion will take place from March 7-11.  This first phase is intended to facilitate meeting with members of the community and start a discussion about building possible connections.
  2. The second IN-PERSON portion (envisioned for the end of 2022) will advance the discussion and establish explicit steps of how both MolSSI scientists and community members can work together.

The challenges that appeal both to the materials science and quantum chemistry community are the following:

  • Different bases (plane wave, atomic bases, finite element, numerical bases, LAPW)
  • Ease of development outside of established packages (periodic integrals)
  • Development of post-DFT approaches and computational affordability of post-DFT methods
  • Connections to HPC community
  • Availability of benchmarks both for DFT and post-DFT methods
  • Tools for machine learning
  • Collection of data (established vs new)

On-line workshop format: 5 days, 4 speakers per session, panel discussion to facilitate finding how MolSSI can contribute and be engaged with the community. This workshop should engage both materials scientists and quantum chemistry community members interested in working on solid state problems.

Confirmed Speakers

  • Lorenzo Machino
  • Volker Blum
  • Sandeep Sharma
  • Giulia Gali
  • Jeff Neaton
  • Eran Rabani
  • Vojtech Vlacek
  • Heather Kulik
  • Kieron Burke
  • Francesco Paesani
  • Robert DiStasio
  • Annabella Selioni
  • Tim Berkelbach
  • Andreas Grueneis
  • Patrick Rinke
  • Shiwei Zhang
  • Noa Marom
  • Tianyu Zhu

Registration for the Virtual Workshop is required via THIS LINK.

Questions about the workshop can be directed to Prof. Zgid.

The Molecular Sciences Software Institute (MolSSI) and NVIDIA Deep Learning Institute (DLI) invite you to register for upcoming hands-on on workshops in high-performance computing and machine learning:

The number of seats are limited and in order to ensure the quality of these workshops, we will not extend the registration capacity. Therefore, we encourage everyone to sign up as early as possible.

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

MolSSI Workshops

The MolSSI’s Software Workshop program is a community-driven effort in which researchers from academia, industry, and national labs propose timely and important topics focused on the software needs of the molecular sciences, and the MolSSI organizes or facilitates the event.