Amber Free Energy Workshop Program (Tentative)
List of covered topics
Day 1 - Introduction to force fields, visualization, and Amber
Day 2 - Molecular simulations with Amber
Day 3 - QM/MM simulations and potential of mean force
Day 4 - Alchemical free energy methods
Day 5 - Machine learning enhanced free energy simulations
Instructors
Solen Ekesan, Rutgers University
Ryan Snyder, Rutgers University
Jinzhe Zeng, Rutgers University
William Betancourt, Michigan State University
Majid Jafari, Michigan State University
Andreas Goetz (AG), San Diego Supercomputer Center
Metin Aktulga (MA), Michigan State University
Kennie Merz (KM), Cleveland Clinic Foundation
Darrin York (DY), Rutgers University
Program
Daily program is a mix of lectures (L) and hands-on (H) sessions.
Program is subject to change.
Times listed below are US Pacific Time.
Location for all lectures and hands-on sessions are
the SDSC Auditorium on UCSD Campus.
Day 1 (Monday) - Introduction to force fields, visualization, and Amber
08:30 - 09:00 Light Breakfast & Check-in
09:00 - 10:00 Welcome and Introductions (AG)
10:00 - 10:45 Intro to HPC and SDSC Expanse (L)(AG)
10:45 - 11:15 Coffee break
11:15 - 12:00 Introduction to force fields and molecular dynamics (L)(MA)
12:00 - 13:30 Lunch
13:30 - 14:15 Overview of the AMBER package and its programs (L)(AG)
14:15 - 15:00 Hands-on session 1 (Using VMD to visualize AMBER simulations)
15:00 - 15:30 Coffee break
15:30 - 17:00 Ctd Hands-on session 1 (Using VMD to visualize AMBER simulations)
17:00 - 19:00 Reception @ SDSC Patio
Day 2 (Tuesday) - Molecular simulations with Amber
08:30 - 09:15 Getting started with Amber (L)(DY)
09:15 - 09:30 Coffee break
09:30 - 12:00 Hands-on session 2 - (Introduction to MD simulations using AMBER)
12:00 - 13:30 Lunch
13:30 - 15:00 Hands-on session 3 - (Building protein-ligand complexes with non-standard residues)
15:00 - 15:30 Coffee Break
15:30 - 17:00 Ctd Hands-on session 3 - (Building ribozyme-substrate complexes)
17:30 - 18:30 Round table discussion
Day 3 (Wednesday) - QM/MM and potential of mean force
08:30 - 09:15 Introduction to QM/MM (L)(AG)
09:15 - 10:00 Free energy surface and MFEP methods (L)(DY)
10:00 - 10:30 Coffee break
10:30 - 11:15 Practical considerations for umbrella sampling calculations (L)(DY)
11:15 - 12:15 Hands-on session 4 - (QM/MM PMF using SCC-DFTB, Part 1)
12:15 - 13:00 Lunch
13:00 - 14:30 Ctd Hands-on session 4 - (QM/MM PMF using SCC-DFTB, Part 2)
14:30 - EOD Free time, attendees on their own (see below for sites to help guide you)
Day 4 (Thursday) - Alchemical free energy methods
09:15 - 10:00 Alchemical free energy methods for drug discovery (L)(DY)
10:00 - 10:45 Advanced free energy methods and free energy workflows (L)(DY)
10:45 - 11:15 Coffee break
11:15 - 12:00 Practical considerations for running AFE calculations (L)(DY)
12:00 - 12:15 Group picture
12:15 - 13:30 Lunch
13:30 - 15:00 Hands-on session 5 - (AFE simulations for RBFE and ABFE calculations)
15:00 - 15:30 Coffee break
15:30 - 17:00 Ctd Hands-on session 5 - (AFE simulations for RBFE and ABFE calculations)
17:00 - 20:00 Conference dinner @ UC San Diego, Seventh College, 15th floor
Day 5 (Friday) - Machine learning enhanced free energy simulations
08:30 - 09:15 Introduction to machine learning models for molecular simulations (L)(MA)
09:15 - 10:00 Using ML potentials in QM/MM free energy surface and bookending studies (L)(DY)
10:00 - 10:30 Coffee break
10:30 - 11:15 Practical considerations for running QM/MM book-ending and PMF calculations (L)(DY)
11:15 - 12:00 Industry Guest Lecture - Chuan Tian, Tandem AI
Improving reliability of BFE calculations with enhanced sampling approach
12:00 - 13:30 Lunch
13:30 - 15:00 Hands-on session 6 - (QM/MM bookending / PMF studies)
15:00 - 15:30 Coffee break
15:30 - 16:30 Ctd Hands-on session 6 - (QM/MM bookending / PMF studies)
16:30 - 17:00 Final Remarks / Question and Answer Session
Hands-on Exercises Credits
Lauren Lerew, Rutgers University
Erika McCarthy, Rutgers University
Jinzhe Zeng, Rutgers University
Ryan Snyder, Rutgers University
Tim Giese, Rutgers University
Solen Ekesan, Rutgers University
Darring York, Rutgers University
Things to do around San Diego
https://www.sandiego.org/
https://www.visitcalifornia.com/places-to-visit/san-diego/
https://www.cntraveler.com/gallery/best-things-to-do-in-san-diego
https://www.planetware.com/tourist-attractions-/san-diego-us-ca-sd.html
https://www.alltrails.com/us/california/san-diego
https://urbanoutdoors.com/hiking-in-near-san-diego/
https://www.sandiego.org/articles/breweries/san-diego-breweries.aspx
https://www.thrillist.com/drink/san-diego/best-breweries-san-diego
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