Computational Biophysics Workshop - Bremen, Oct. 17-21, 2011

Program

Locations:
  • Conference Hall, Campus Center, Campusring 1, Jacobs University Bremen

Mon, 10/17: Introduction to Protein Structure and Dynamics - Klaus Schulten

08:00-08:45 Registration
08:45-09:00 Welcome and Brief Overview - Ulrich Kleinekathoefer
09:00-09:10 Opening Remarks
09:10-10:40 Structure and Sequence Analysis with VMD
Coffee Break  
11:00-12:00 Introduction to Molecular Dynamics with NAMD
12:00-12:20 Q & A
Lunch Break  
14:00-16:00 VMD Tutorial - Using VMD; NAMD Tutorial
Coffee Break  
16:15-18:00 VMD Tutorial - Using VMD; NAMD Tutorial

 

Tue, 10/18: Statistical Mechanics of Proteins - Klaus Schulten

09:00-10:30 Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD
Coffee Break  
10:50-12:00 Exemplary Applications of VMD / NAMD in Modern Research
12:00-12:30 Q & A; Group photo
Lunch Break  
14:00-16:00 Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**
Coffee Break  
16:15-18:00 Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**

 

Wed, 10/19: Introduction to Bioinformatics and Forcefields - Klaus Schulten, Emad Tajkhorshid

09:00-10:30 Introduction to Structure and Sequence Alignment (K. Schulten)
Coffee Break  
10:50-12:00 Introduction to Topology, Parameters, and Structure Files, Part I (E. Tajkhorshid)
12:00-12:20 Q & A
Lunch Break  
14:00-16:00

Participant tutorial options:
1) Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool, or
2) NAMD Tutorial & Stretching Deca-alanine, or
3) Expert NAMD Set Tutorials*, or
4) Free Energy Set Tutorials**, or
5) Participants work on their own projects
Coffee Break  
16:15-18:00 Participant tutorial options:
1) Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool, or
2) NAMD Tutorial & Stretching Deca-alanine, or
3) Expert NAMD Set Tutorials*, or
4) Free Energy Set Tutorials**, or
5) Participants work on their own projects

 

Thu, 10/20: Parameters for Classical Force Fields - Emad Tajkhorshid

09:00-10:30 Introduction to Topology, Parameters, and Structure Files, Part II
Coffee Break  
10:50-12:00 Examples and Applications
12:00-12:20 Q & A
Lunch Break  
14:00-16:30 Parameterizing a Novel Residue
Coffee Break  
16:45-18:00 Topology File Tutorial

 

Fri, 10/21: Simulating Membrane Channels - Emad Tajkhorshid

09:00-10:30 Introduction and Examples
Coffee Break  
10:50-12:00 Transport in Aquaporins; Nanotubes
12:00-12:20 Q & A
Lunch Break  
14:00 -16:00 Participant tutorial options:
1) Membrane Proteins & Simulation of Water Permeation Through Nanotubes, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**
Coffee Break  
16:15-18:00 Participant tutorial options:
1) Membrane Proteins & Simulation of Water Permeation Through Nanotubes, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**

 

Tutorial Options:
* Expert NAMD Set Tutorials:
     - Shape-Based Coarse Graining
     - User-Defined Forces in NAMD, or
** Free Energy Set Tutorials
     - A Tutorial to Set Up Alchemical Free Energy Perturbation Calculations in NAMD
     - A Tutorial to Set Up Adaptive Biasing Force Calculations in NAMD

Click here to see descriptions of tutorials listed in program.

Note: program subject to change.