AMBER Workshop - August 22 to 26, 2011 - Shanghai, China
Program

The workshop will start at 9AM on Monday, August 22, 2011 and finish at 5PM on Friday, August 26, 2011. Each of the five workshop days will consist of approximately 3 hours of lectures and 5 hours of practical exercises in the form of hands-on-tutorials on local workstations.

The workshop will take place in Room 200 of the ECNU Computer Science Building (click here for a campus map)

The official workshop language (including all course materials) will be English (limited support during the hands-on sessions can also be provided in Chinese).

Linux workstations with all required software will be provided for the hands-on sessions. Personal laptops are not required. While AmberTools is available for free, the AMBER software package is officially distributed by UCSF subject to a licensing agreement. The workshop will use version 11 of AMBER and version 1.5 of AmberTools.

Instructors: Ross Walker (RW), Andreas Goetz (AG)
Tutors: Ye Mei, (YM), Yun Xiang, (YX), Xingyu Wang (XW)
(L) = Lecture, (H) = Hands on Tutorial

Day 1 (Monday 22nd Aug 2011)

9:00 - 9:45 Registration.  
9:45 - 10:00 Welcome / Introduction to the Workshop. (L)  
10:00 - 10:45 Introduction to force fields and molecular dynamics. (Part 1) (L) RW
10:45 - 11:15 Coffee break.  
11:15 - 12:00 Introduction to force fields and molecular dynamics. (Part 2) (L) RW
12:00 - 13:30 Lunch.  
13:30 - 14:15 Overview of the AMBER package and its programs. (L) RW
14:15 - 17:00 Hands-on session 1 - (Introduction to molecular dynamics simulations using AMBER) (H) RW/AG/YM/YX/XW

Day 2 (Tuesday 23rd Aug 2011)

8:30 - 10:00 Hands-on session 2 - (Using VMD to visualize AMBER simulations) (H) RW/AG/YM/YX/XW
10:00 - 10:45 Overview of AMBER Force Fields and Solvent Models. (L) RW
10:45 - 11:15 Coffee break.  
11:15 - 12:00 Dealing with non-standard residues. (L) RW
12:00 - 13:30 Lunch.  
13:30 - 15:30 Hands-on session 3 - (Building protein-ligand complexes containing non-standard residues with Antechamber) (H) RW/AG/YM/YX/XW
15:30 - 16:15 Designing a good simulation project (L) RW
16:15 - 17:00 What if there is no crystal structure? (L) RW

Day 3 (Wednesday 24th Aug 2011)

8:30 - 9:15 Practical Guide to Running MM/PBSA calculations (L) AG
9:15 - 10:45 Hands-on session 4 - (Introduction to binding energy calculations using MM-PBSA) (H) RW/AG/YM/YX/XW
10:45 - 11:15 Coffee Break.  
11:15 - 12:00 Hands-on session 4 - (Introduction to binding energy calculations using MM-PBSA) Contd (H) RW/AG/YM/YX/XW
12:00 - 12:15 Group Picture.  
12:15 - 13:30 Lunch.  
13:30 - 14:20 Statistical Mechanics for Free Energy Calculations (L) AG
14:20 - 17:00 Hands-on session 5 - (Calculating relative binding free energies for protein/carbohydrate complexes) (H) RW/AG/YM/YX/XW

Day 4 (Thursday 25th Aug 2011)

8:30 - 9:15 An overview of enhanced sampling techniques (L) AG
9:15 - 9:45 Practical considerations for running replica exchange calculations (L) RW
9:45 - 10:45 Hands-on session 6 - (Replica exchange simulations) (H) RW/AG/YM/YX/XW
10:45 - 11:15 Coffee Break.  
11:15 - 12:00 Hands-on session 6 - (Replica exchange simulations) Contd (H) RW/AG/YM/YX/XW
12:00 - 13:30 Lunch  
13:30 - 15:15 Hands-on session 6 - (Replica exchange simulations) Contd (H) RW/AG/YM/YX/XW
15:15 - 15:45 Guest Lecture - Allan Hou [NVIDIA Inc.] (L) AH
15:45 - 16:30 Considerations for Maximizing Performance (Parallel Execution and NVIDIA GPU Acceleration) (L) RW
16:30 - 17:00 Practical considerations for running umbrella sampling calculations (L) AG
     
18:00 - 22:00 Workshop Social / Dinner  
  Park Café, Shanghai Marriott Hotel Changfeng Park, 158 Da Du He Road, Putuo District  

Day 5 (Friday 26th Aug 2011)

9:30 - 10:45 Hands-on session 7 - (Umbrella sampling simulations) (H) RW/AG/YM/YX/XW
10:45 - 11:15 Coffee Break.  
11:15 - 12:00 Hands-on session 7 - (Umbrella sampling simulations) Contd (H) RW/AG/YM/YX/XW
12:00 - 13:30 Lunch  
13:30 - 14:15 An Introduction to QM/MM Calculations (L) AG
14:15 - 16:30 Hands-on session 8 - (QM/MM MD Simulations) (H) RW/AG/YM/YX/XW
16:30 - 17:00 Final Remarks / Question and Answer Session RW/AG

List of covered topics
  1. Introduction to force fields and molecular dynamics (Lecture)
  2. Overview of AMBER and AmberTools and its programs (Lecture)
  3. Introduction to setting up and running simulations (Lecture / Hands on)
  4. Visualizing AMBER simulations (Hands on)
  5. Overview of AMBER Force Fiels / Solvent Models etc. (Lecture)
  6. Introduction to implicit solvent and binding energy calculations (Lecture)
  7. Protein folding and advanced analysis (Hands on)
  8. Designing good simulation projects (Lecture)
  9. Dealing with non-standard residues (Lecture / Hands on)
  10. What to do if there is no crystal structure (Lecture)
  11. Statistical mechanics for free energy calculations (Lecture / Hands on)
  12. QM/MM coupled potential simulations (Lecture / Hands on)
  13. GPU accelerated molecular dynamics simulations (Lecture)
Suggested reading

The following material is a non-exhaustive, fairly subjective list of information about the AMBER programs and computational chemistry in general. It is not a prerequisite for workshop participants but shall serve as a pointer for the interested.

  1. AMBER 11 manual
  2. AmberTools manual

  3. D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. "The AMBER biomolecular simulation programs." J. Comput. Chem. 26 (2005) 1668-1688.

  4. J.W. Ponder and D.A. Case. "Force fields for protein simulations." Adv. Prot. Chem. 66 (2003) 27-85.

  5. O.M. Becker, A.D. MacKerrell, Jr., B. Roux, M. Watanabe, eds, "Computational Chemistry and Biophysics", Marcel Dekker, 2001: Chapter 3 "Dynamics Methods" pp39-67.

  6. O.M. Becker, A.D. MacKerrell, Jr., B. Roux, M. Watanabe, eds, "Computational Chemistry and Biophysics", Marcel Dekker, 2001: Chapter 9 "Free Energy Calculations" pp169-197.

  7. Andrew R. Leach, "Molecular Modelling - Principles and Applications", 2nd Edition (2001), Prentice Hall, Harlow, UK.

  8. Daan Frenkel and Berend Smit, "Understanding Molecular Simulation" 2nd Edition (2001), Academic Press, London, UK.

  9. Frank Jensen, "Introduction to Computational Chemistry", 2nd Edition (2006), Wiley VCH, Chichester, UK.