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Applications of Free Energy Methods

Amber Free Energy Workshop

Free energy (FE) simulations are a particularly important and effective class of molecular simulation method used to study chemical processes such as drug binding, protein folding, protein-protein interactions, allosteric activation, gas adsorption and diffusion in metal–organic frameworks (MOFs), piezoelectric responses or catalytic chemical events. Theoretical methods to improve the accuracy and efficiency of free energy estimations is an active research area. Applications of free energy methods continue to grow as computational power and theoretical frameworks improve. However, free energy calculations are often complex to setup and execute.

Through a series of lectures and hands-on exercises, this workshop aims to ensure that computational scientists interested in free energy methods can learn the best practices in carrying out accurate, efficient and reliable free energy studies.

  • Workshop (in-person): Monday, August 12 – Friday, August 16, 2024

  • Location: SDSC Auditorium, UC San Diego Campus

  • Application deadline: June 7 June 23 (Notifications: June 28)

  • Registration costs:
    ▫ Academic, Student, Government and Non-Profit Organizations: $350
    ▫ Industry: $600
    ▫ Registration fees are due only after an application is accepted.

Registration fees help support workshop organization. Registration includes a reception, conference dinner, and coffee, snacks and light refreshments during breaks.

Apply Here!


The workshop will start at 8:30 AM on Monday, August 12, 2024, and finish at 5:00 PM on Friday, August 16, 2024. Each of the five workshop days will consist of a mix of lectures and intensive hands-on sessions designed around the lecture topics. Additionally, we will have guest speakers to cover applications and opportunities using free energy methods in industry.

The workshop will take place in the auditorium of the San Diego Supercomputer Center (SDSC) on the campus of the University of California, San Diego. See here for SDSC visitor information.

Daily program:

    ▪ 8:30 - 12:00 - Morning session (two sessions w/coffee break)
    ▪ 12:00 - 13:30 – Lunch
    ▪ 13:30 – 17:00 – Afternoon session (two session w/coffee break)

There will be a conference reception and conference dinner.

List of covered topics:

    Day 1 - Introduction to force fields and molecular simulations
    Day 2 - Visualization and high fidelity simulations
    Day 3 - QM/MM simulations and potential of mean force
    Day 4 - Alchemical free energy methods
    Day 5 - Machine learning enhanced free energy simulations

A detailed list of lectures and exercise material will be made available on a Github repository once we are drawing closer to the workshop date.

Hands on exercises will use the Expanse supercomputer. Participants will need laptop computers to connect to Expanse for the hands-on sessions.

Prior HPC Experience: Participants are expected to have experience with Linux and HPC basics. For those who are not familiar with Linux and HPC, a tutorial with the prerequisite information will be shared ahead of the workshop.


Workshop Venue

The workshop will take place in the auditorium of the San Diego Supercomputer Center (SDSC) on the campus of the University of California, San Diego. See here for SDSC visitor information.


On-campus housing is being arranged to keep participation costs as low as possible. On-campus housing will be available for a nightly rate of $110/person for all participants. Please indicate in your application whether you plan to make use of campus housing as we need to reserve sufficient space.

Alternatively, nearby hotels are available around the UCSD campus. We will update the website in the near future with a list of recommended hotels.

Housing and Travel Support

Support for on-campus housing and/or domestic flights may be provided depending on the availability of funds. At the moment we cannot guarantee any support. Participants from underrepresented groups and minority serving institutions will receive priority. Please indicate your preference to be considered for support during registration.

Organizers and Contact Information

"How's that for maxed out?"

Last modified: Jun 6, 2024