| Instructors: | Dr. Charles L. Brooks III , The Scripps Research Institute |
| Dr. Michael Crowley, The Scripps Research Institute | |
| Dr. Alexander D. MacKerell, Jr., University of Maryland at Baltimore | |
| Nilesh Banavali, University of Maryland at Baltimore |
A complete agenda follows the list of lectures and tutorials.
| Lectures | Tutorials | |
|---|---|---|
| Overview of Molecular Modeling and Dynamics (PDF file, 2.8 Mb) | Building and Conditioning Macromolecular Structures for Proteins | |
| Periodic Boundaries, Non-bond Interactions and PME (PDF file, 4.6 Mb) | ||
| Simulations of Nucleic Acids and Lipids (PDF file, 61K) | Building and Conditioning Macromolecular Structures for DNA | |
| Building and Conditioning Macromolecular Structures for Membranes | ||
| Conformational Search, Structure, and Trajectory Analysis (PDF file, 3.4 Mb) | ||
| Strategies for Parameter Development (PDF file, 71K) | Parameterization of Molecules | |
| Free Energy Simulations (PDF file, 3.4 Mb) | Free Energy Calculations | |
| Hybrid Quantum Mechanical/Molecular Mechanical Methods (PDF file, 27K) | Hybrid Quantum Mechanical/Molecular Mechanical Calcuations | |
| Merck Molecular Force Field (PDF file, 23K) | Merck Molecular Force Field Calculations |
| 1:00 - 1:15 | Welcome, administrative details | Troy Wymore | |
| 1:15 - 1:45 | Introduction & overview of biomedical computing at PSC | David Deerfield | |
| 1:45 - 2:00 | Break | ||
| 2:00 - 3:00 | Introduction to the PSC environment: UNIX, AFS, file archiving, Cray T3E | Tom Maiden | |
| 3:00 - 5:00 | Computer Laboratory: Tutorials, setting up a working environment for the workshop |
| 8:30 - 9:00 | Continental breakfast | ||
| 9:00 - 9:15 | Welcoming remarks | Ralph Roskies, Scientific Director | |
| 9:15 - 10:15 | Overview of molecular modeling and dynamics (PDF file, 2.8Mb) |
Charles Brooks | |
| 10:15 - 10:30 | Break | ||
| 10:30 - 11:30 | Periodic boundaries, nonbond interactions, and PME (PDF file, 4.6 Mb) |
Michael Crowley | |
| 11:30 - 12:30 | Simulations of nucleic acids and lipids (PDF file, 61K) |
Alex MacKerell | |
| 12:30 - 2:00 | Lunch and poster session | ||
| 2:00 - 4:00 |
Hands on session building and "conditioning" macromolecular structures
�Proteins
�DNA �Membranes |
||
| 4:00 - 4:15 | Break | ||
| 4:15 - 5:15 | Conformational search, Structure and trajectory analysis (PDF file, 3.4 Mb) |
Michael Crowley |
| 8:30 - 9:00 | Continental breakfast | ||
| 9:00 - 10:30 | Strategies for parameter development (PDF file, 71K) |
Alex MacKerell | |
| 10:30 - 10:45 | Break | ||
| 10:45 - 12:15 | Computer laboratory | ||
| 12:15 - 1:30 | Lunch | ||
| 1:30 - 2:45 | Free energy simulations (PDF file, 3.4 Mb) |
Charles Brooks | |
| 2:45 - 3:00 | Break | ||
| 3:00 - 5:15 | Computer laboratory: CHARMM Examples | ||
| Break for dinner | |||
| 7:00 - 9:00 | Trip to the Westinghouse machine room facility |
| 8:30 - 9:00 | Breakfast | ||
| 9:00 - 10:00 | Quantum mechanical / molecular mechanical hybrid methods (PDF file, 27K) and Merck molecular force field (PDF file, 23K) |
Alex MacKerell | |
| 10:15 - 11:45 | Question/answer and discussion session or computer lab | ||
| 11:45 - Noon | Evaluations | ||
| Noon - 1:00 | Lunch | ||
| Afternoon | Optional hands-on |
