Hands-On Workshop on Computational Biophysics using VMD and NAMD
Location: Bremen
Organisers
The workshop sets out to explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and free-energy methods to address rare events. During the proposed hands-on workshop, participants will use the scalable molecular dynamics program NAMD and the visualization platform VMD. NAMD and VMD are currently utilized by, respectively, 47,000 and 195,000 end-users worldwide, with a growing demand for didactic events covering introductory to advanced material. While such events are generally organized on the American continent, it is important that they also be held at European venues.
The primary objective of this tutorial is to teach the participant how to use NAMD and VMD for biomolecular modeling. NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to thousands of processors on high-end parallel architectures and hundreds of processors on commodity clusters. The program VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, or lipid-bilayer assemblies. It may be used to view more general molecules, as VMD can read a host of formats, including standard Protein Data Bank (PDB) files, and display the contained structure. VMD provides a wide variety of methods for rendering and coloring molecules and can be used to animate and analyze the trajectory of a molecular dynamics simulation. More details, references and training material for both, NAMD and VMD, can be found at http://www.ks.uiuc.edu/
Mon, June 16: Introduction to Protein Structure and Dynamics - Klaus Schulten
08:30-09:00 Registration
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
Dinner Break
19:30-21:00 Contributions from participants
Tue, June 17: Introduction to Bioinformatics - Zaida Luthey-Schulten
09:00-10:30 Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD
Coffee Break
10:50-12:00 Application of MultiSeq to Evolution of Translation Machinery
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) Expert Sequence Analysis
- Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes
- Evolution of Translation EF-Tu: tRNA
- Evolution of Translation: The Ribosome; or
3) Dynamical Network Analysis
4) 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) Expert Sequence Analysis
- Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes
- Evolution of Translation EF-Tu: tRNA
- Evolution of Translation: The Ribosome; or
3) Dynamical Network Analysis
4) Participants work on their own projects
Dinner Break
19:30-21:00 Contributions from participants
Workshop Participant Short Lectures
21:00-21:30 Cloud Computing Opportunities for Computational Investigators (Amazon) - Ryan McGreevy
Wed, June 18: Statistical Mechanics of Proteins - Klaus Schulten
09:00-10:00 Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD
10:00-10:45 Applications of VMD / NAMD in Modern Research
Coffee Break
11:00-12:00 Introduction to GPU Accelerated NAMD Simulation - K. Schulten, R. McGreevy
12:00-12:30 Q & A; Group picture
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**
4) GPU Accelerated Molecular Dynamics and Visualization Tutorial
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**
4) GPU Accelerated Molecular Dynamics and Visualization Tutorial
Thu, June 19: Parameters for Classical Force Fields - Emad Tajkhorshid
09:00-10:30 Introduction to Topology, Parameters, and Structure Files
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
Dinner Break
19:30-21:00 Contributions from participants
Fri, June 20: 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**
References
Ulrich Kleinekathöfer (Jacobs University Bremen) - Organiser
United States
Chris Chipot (University of Illinois at Urbana-Champaign, USA) - Organiser
Jodi Hadden (University of Illinois at UrbanaChampaign) - Organiser