Computational Biophysics Workshop - Pittsburgh, May 19-23, 2014
Computing labs will be set up for use during the workshop. However, those wishing to bring their own laptop for use in the workshop can follow the instructions below to have it set up for the event. Read into the starting sections of each tutorial to see required software and files.
I. Install Software
Tutorial sessions use the VMD - version 1.9.1, NAMD - version 2.9, and ProDy 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. Some tutorials suggest additional software programs (read introductory sections of tutorials). 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
- GPU Tutorial (pdf, 443 KB) (required tutorial files [tar.gz, 1 GB])
or
- 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)
Day 3: Computational Nano-Bio - Alek Aksimentiev
- Modeling Nanopores for Sequencing DNA: (pdf, 15M), (required tutorial files, [.tar.gz, 277M])
- Introduction to MD Simulation of DNA-protein Systems: (pdf, 4.4M) (required tutorial files [.tar.gz, 438M])
Day 4: Collective Dynamics of Proteins Using Elastic Network Models - Ivet Bahar, Tim Lezon and Ahmet Bakan
- ProDy Tutorial
- NMWiz Tutorial
- ENM Analysis
- Ensemble Analysis
- Structure Analysis
- Trajectory Analysis
- Conformational Sampling
- See also the main tutorial page
Day 5: Druggability Simulations, and Analyzing Sequence Patterns and Structural Dynamics - Ivet Bahar and Ahmet Bakan
- Druggability Tutorial
- Evol Tutorial
- See also the main tutorial page
