Programme

EMBO Practical Course on Biomolecular Simulation

Last updated: 29.06.2000
Lectures (mostly on theory) [L] and Evening Lectures (mostly on current/recent research) [EL] will be given in Room 202.
The practicals [P] will take place in the Computer Teaching Lab.

Fixed times are:
8:45 Bus transfer from the ISG Hotel to EMBL
10:15-10:30 Coffee Break between Lectures (Operon Foyer/202)
12:00 Lunch
15:30-16:00 Coffee Break between Practicals (Biocomputing Seminar Room)
19:00 Dinner (except 9th & 12th)

Wednesday, July 5
Arrival
15:45  Bus transfer from the ISG Hotel to EMBL
16:00  [L0] Introduction & Presentation of participants (5min/person with 1 overhead transparency)  everybody
19:00  Dinner 
20:00  [P0] Introduction to EMBL computing environment  Schmitz
21:00  Beer/Juice etc in Biocomputing Seminar room 
22:15 Bus transfer to hotel
Thursday, July 6
morning
9:00  [L] Modelling: Sequence analysis and mutation Wodak 
10:30  [L] Molecular mechanics: energy minimization Fischer
afternoon
13:00  [P1] Energy calculation and minimization Wade
evening
20:00  [EL] Force probe molecular dynamics simulations Grubmuller
21:15  Bierhelderhof
Friday, July 7
morning
9:00  [L] Normal mode analysis:Theory +application  Fischer
9:30  [L] Normal mode analysis:Application  Hinsen
10:30 [L] Molecular dynamics and essential dynamics  Grubmuller 
afternoon
13:00 [P2a] Domain motions in large proteins by normal mode analysis Hinsen
16:00 [P2b] Molecular dynamics, Essential dynamics Wade, Luedemann
evening
20:00  [EL] Molecular dynamics simulation of peptide folding, stability and aggregation Mark
21:15 Bus transfer to hotel
Saturday, July 8
morning
9:00  [L] When all else fails: do-it-yourself programming Hinsen 
10:30  [L] Free energy calculations  Mark 
afternoon
13:00 [P3a] Code-writing Hinsen
16:00 [L] MolCad advanced visualization demo Matthias Keil
16:30 [P3b] Free energy calculations Wade
evening
20:00  [EL] Molecular dynamics in free energy calculations and enzyme catalysis Kollman
21:15 Bus transfer to downtown Heidelberg
Sunday, July 9
morning
9:00  [L] Force fields Kollman
afternoon: EXCURSION
10:45  Bus transfer from EMBL to Neckar river (Stadthalle)
11:00  Boat trip from Heidelberg to Neckarsteinach 
12:20  Hiking uphill to Dilsberg castle (ca. 1-1.5h)
13:30  Lunch in Dilsberg 
17:00  Boat trip from Neckarsteinach back to Heidelberg
evening
free
Monday, July 10
morning
9:00  [L] High performance/parallel computing Schmitz
9:45  [L] Parallel MD + Visualization  Schulten
afternoon
13:00  [P4] VMD/NAMD/SMD Schulten 
evening
20:00  [EL] Molecular recognition: simulation and informatics Gilson
21:00 [EL] Molecular simulations using hybrid potentials Field
22:15 Bus transfer to hotel
Tuesday, July 11
morning
9:00  [L] Electrostatics Gilson
10:30  [L] Brownian dynamics Wade
afternoon
13:00  [P5] Electrostatics and Brownian dynamics Gilson,Wade
evening
20:00  [EL] Steered Molecular Dynamics: A Powerful Method for Molecular Biology Schulten
21:15 Bus transfer to hotel
Wednesday, July 12
morning
9:00  [L]  Computation/comparison/validation of experimental quantities  Smith
10:30  [L]  QMMM Field
afternoon
13:00  [P6] QMMM (Dynamo) Field 
16:30  Round Table:
  • Questions & discussion (questions submitted over course by participants)
  • Long range forces: cutoffs, PME, FMA etc
  • The sampling problem
  • Bottlenecks
  • Simulation in the context of genomics/proteomics 
    		•  everybody 
    evening
    19:15  Bus transfer from EMBL to Heidelberg
    19:30  Social Dinner: Restaurant "Vetters" in Heidelberg (or Neuenheim) 
    Thursday, July 13
    9:00  [L] Modelling in NMR structure determination Nilges
    10:30 [P7] Structure  calculation and refinement (CNS) Nilges
    12:30  [L] How to choose the appropriate simulation method, Summary, Future developments  3 speakers
    13:00  Lunch 
    Departure