Computational Biophysics Workshop - Pittsburgh, May 19-23, 2014

The workshop will provide computer stations for completion of tutorials. Those wishing to bring a laptop should make sure the laptop configuration meets or exceeds the requirement below. Configurations that provide less than the minimum requirements may function poorly, or not at all.

Hardware Requirements

  • Windows
    • Operating System: Windows 7, Vista, XP or 2000
    • Memory: 512 MB RAM
    • Processor: Pentium 4 2.4 Ghz CPU (or comparable)
    • Graphics card: nVidia Geforce Ti4600, or comparable
  • Mac
    • Operating System: Mac OS X 10.3 or greater
    • Memory: 512 MB RAM
    • Processor: G4 Processor or any Intel Mac
    • Graphics card: Macintosh computers often come with sufficient graphics processing power, so no additional card is necessary
  • Linux
    • Operating System: Any reliable Linux distribution released within the last three years.
    • Memory: 512 MB RAM
    • Processor: Pentium 4 2.4 Ghz CPU (or comparable)
    • Graphics card: nVidia Geforce Ti4600, or comparable

Please note the above are bare minimum requirements; more power and memory is desirable for all the above systems. For example, 512 MB RAM on a Mac will be functional, but very slow-going through the tutorials!

Software Requirements

Below are minimum software requirements. Consult each tutorial for any suggested additional software(s).

Visual Molecular Dynamics - VMD
For molecular modelling, the tutorials use VMD. You can download the latest version of VMD for your operating system from http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD. See the User and Installation guides for installation instructions.

Nanoscale Molecular Dynamics - NAMD
For numerical simulation, the tutorials use NAMD. You can download the latest version of NAMD for your operating system from http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD. See the NAMD User's Guide for installation and usage instructions.

ProDy - Protein Dynamics and Sequence Analysis
For protein dynamics and sequence analysis, use ProDy. You can download the latest version of ProDy for your operating system from http://www.csb.pitt.edu/prody/getprody.html. Documentation about ProDy is available here.

Plotting Program
For some tutorials, a program for plotting graphs is necessary. Some recommended utilities include:

Text Editor
A basic text editor program is used in some tutorial. Most likely one came with your operating system. Some options for editors are liste below:
  • Windows: NotePad
  • Unix: nedit
  • Mac: TextEdit