Computational Biophysics Workshop - Urbana, April 5-7, 2018

Laptop Requirements

The TCBG Workshop Tutorials require up-to-date hardware, operating systems, and software versions. The molecular calculations proposed during this workshop will be executed using the computing power delivered by the Amazon Web Servers cloud services. The preferred operating system for optimal results and software usability is Linux. Users of other operating systems will be able to follow the instructions using the Amazon cloud service EC2 virtual machine. Minimum requirements for laptops are provided below. Configurations that provide less than the minimum requirements may function poorly, or not at all.

Hardware Requirements

  • Windows
    • Operating System: 7,8 or 10
    • Memory: 2 GB RAM
    • Processor: Intel Core 2 Duo 2.0 Ghz CPU (or comparable)
    • Graphics card: NVIDIA GeForce 320M, or comparable
  • Mac
    • Operating System: Mac OS X 10.4.7 or later
    • Memory: 2 GB RAM
    • Processor: Intel Core 2 Duo 2.0 Ghz CPU (or comparable)
    • Graphics card: NVIDIA GeForce 320M, or comparable
  • Linux
    • Operating System: Any reliable Linux distribution released within the last three years.
    • Memory: 2 GB RAM
    • Processor: Intel Core 2 Duo 2.0 Ghz CPU (or comparable)
    • Graphics card: NVIDIA GeForce 320M, or comparable

Software Requirements

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 (nightly build) from: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD. See the NAMD User's Guide for installation and usage instructions.

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