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.
Program
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.
Logistics
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.
Housing
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
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