Computational Biophysics Workshop - Urbana, Feb. 11-15, 2012
Laptop Setup
This page describes how workshop participants should set up their laptops for participation in workshop hands-on tutorial sessions.
I. Install Software
Tutorial sessions use the VMD - version 1.9 and NAMD - version 2.7 or higher software packages, plus plotting programs (e.g., Excel on Windows, XMGrace on Unix/Mac) and text editors (e.g, Notepad on Windows, nedit on Unix, TextEdit on Mac) as described on the laptop requirements page. Be sure that all your software is installed and tested before you arrive at the workshop - there is no time on site for installation troubleshooting.II. Install Tutorials Texts and Files
Each tutorial consists of a text in pdf format, and computer files used in the tutorial. Be sure that you have the files you need each day of the tutorial sessions in place before you arrive at the workshop. Files by day of workshop tutorial session are listed below. It is easiest to follow the tutorials if files are placed in a 'Workshop' directory on the desktop.
Day 1 - Introduction to Protein Structure and Dynamics - Klaus Schulten
- Using VMD: (pdf, 1.6M) (required tutorial files [.tar.gz, 44.9M], [.zip, 44.9M], Individual files)
- NAMD Tutorial:
- pdf for Unix/Mac, or pdf for Windows
- required tutorial files (all platforms) [.tar.gz, 148M], [.zip, 148M], individual files (all platforms)
Day 2: Statistical Mechanics of Proteins - Klaus Schulten
- NAMD Tutorial:
- pdf for Unix/Mac, or pdf for Windows
- required tutorial files (all platforms) [.tar.gz, 148M], [.zip, 148M], individual files (all platforms)
- Stretching Deca-alanine: (pdf, 1.8M) (required tutorial files [.tar.gz, 5.3M], [.zip, 5.3M], individual files)
or
- Expert NAMD Set Tutorials
- Shape-Based Coarse Graining: (pdf, 2.4M) (required tutorial files, [.zip, 6.5M], individual files)
- User-Defined Forces in NAMD: (pdf, 4.3M ) (required tutorial files [.tar.gz, 306M], [.zip, 306M], individual files)
or
- Free Energy Set Tutorials
- A Tutorial to Set Up Alchemical Free Energy Perturbation
Calculations in NAMD:
(pdf, 671k) (required tutorial files [.tar.gz, 1.9M], [.zip, 1.9M], individual files) - A Tutorial to Set Up Adaptive Biasing Force Calculations in NAMD:
(pdf, 1.1M) (required tutorial files [.tar.gz, 57k], [.zip, 69k], individual files)
- A Tutorial to Set Up Alchemical Free Energy Perturbation
Calculations in NAMD:
Day 3: Parameters for Classical Force Fields - Emad Tajkhorshid
- Parameterizing a Novel Residue:
(pdf, 2.5M), (required tutorial files (all versions) [.tar.gz, 24.2M], [.zip, 24.2M], individual files (all versions)) - Topology File Tutorial: (pdf, 4.4M ) (required tutorial files [.tar.gz, 11.2M], [.zip, 11.2M], individual files)
Day 4: Simulating Membrane Channels - Emad Tajkhorshid
- Membrane Proteins: (pdf, 1.0M) (required tutorial files: reduced version [.tar.gz, 10.2M]; full version, [.tar.gz, 508M])
- Simulation of Water Permeation Through Nanotubes:
(pdf, 419k) (required tutorial files [.tar.gz, 39.8M], [.zip, 39.8M], individual files)
or
- Expert NAMD Set Tutorials
- Shape-Based Coarse Graining: (pdf, 2.4M) (required tutorial files, [.zip, 6.5M], individual files)
- User-Defined Forces in NAMD: (pdf, 4.3M ) (required tutorial files [.tar.gz, 306M], [.zip, 306M], individual files)
or
- Free Energy Set Tutorials
- A Tutorial to Set Up Alchemical Free Energy Perturbation
Calculations in NAMD:
(pdf, 671k) (required tutorial files [.tar.gz, 1.9M], [.zip, 1.9M], individual files) - A Tutorial to Set Up Adaptive Biasing Force Calculations in NAMD:
(pdf, 1.1M) (required tutorial files [.tar.gz, 57k], [.zip, 69k], individual files)
- A Tutorial to Set Up Alchemical Free Energy Perturbation
Calculations in NAMD:
Day 5: Introduction to Bioinformatics - Zaida Luthey-Schulten
(See instructions here for configuring metadata for MultiSeq - needed for all tutorials)
- Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool:
(pdf, 4.6M) (required tutorial files [.tar.gz, 151M], [.zip, 151M], Individual files)
or
- Expert Sequence Analysis
- Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA
complexes
(pdf, 6.4 MB) (required tutorial files [tar.gz, 268 MB]) - Evolution of Translation EF-Tu: tRNA: (pdf, 3.7 MB) (required tutorial files [tar.gz, 284 MB])
- Evolution of Translation: The Ribosome: (pdf, 1.3 MB) (required tutorial files [tar.gz, 41 MB])
- Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA
complexes
or
- Participants work on their own projects
