Tutorial for the AMBER set of modelling tools.
Location: CECAM-HQ-EPFL, Lausanne, Switzerland
Organisers
The field of molecular modeling is undergoing a slight revolution, with the advent of advanced sampling techniques and accelerators (e.g. GPUs) which promise to bring to the tabletop power only available until now to few people using supercomputers. We have carried three tutorials recently (Shanghai, Barcelona and Dusseldorf) and found that systematically, we have requests for attendance of around 3 to 4 times the available space. This shows us that there is a need for more tutorials like this one.
We will prioritize students/postdocs with some experience in unix-like operating systems and molecular modeling (e.g. QM or MM) but the tutorial will be done at a beginner's level.
The field of molecular modeling is undergoing a slight revolution, with the advent of advanced sampling techniques and accelerators (e.g. GPUs) which promise to bring to the tabletop power only available until now to few people using supercomputers. We have carried three tutorials recently (Shanghai, Barcelona and Dusseldorf) and found that systematically, we have requests for attendance of around 3 to 4 times the available space. This shows us that there is a need for more tutorials like this one.
We will prioritize students/postdocs with some experience in unix-like operating systems and molecular modeling (e.g. QM or MM) but the tutorial will be done at a beginner's level.
To familiarize the attendees with the basic ideas in the molecular dynamics field and to perform hands-on tutorials to allow the users to see how the methods are implemented in the suite of Amber programs. We will go beyond the simple application of methods to instruct the attendees in the proper understanding of the tools and they applicability to certain case. Emphasis will be put into which tools should/can be used for which problems, as well as into reliability and error analysis. The tutorials are made available through the web site for Amber (http://ambermd.org/tutorials/)
Day 1
Introduction to force fields and molecular dynamics. (L)
Overview of Amber and its programs / Setting up a simulation. (L)
AMBER Force Fields and Solvent Models. (L)
Hands-on session 1. Using VMD to visualize AMBER simulations (H)
Hands-on session 2. Using Amber to perform molecular dynamics (H)
Day 2
Designing a good simulation project. (L)
Dealing with non-standard residues. (L)
Statistical Mechanics for Free Energy calculations I (L)
Hands-on session 3. Building protein-ligand complexes containing non-standard residues (H)
Hands-on session 4. Binding energy calculations using MM-PBSA (H)
Day 3
Statistical Mechanics for Free Energy calculations II (L)
Enhanced sampling techniques I (L)
Hands-on session 5. Free Energy Simulations (H)
Hands-on session 6. Umbrella sampling simulations (H)
Day 4
Enhanced sampling techniques II (L)
QM/MM coupled potential simulations. (L)
Hands-on session 7. Replica exchange simulations (H)
Hands-on session 8. QM/MM coupled potential simulations. (H)
Day 5
Study of chemical reactions and conformational changes (L)
Considerations for Maximizing Performance (Parallel Execution and NVIDIA GPU Acceleration) (L)
Hands-on session 9 – Nudged Elastic Band(H)
References
Adrian Roitberg (University of Florida) - Organiser
Jason Swails (University of Florida) - Organiser
Ross Walker (University of California, San Diego) - Organiser