Computational Biophysics Workshop: July 17-21, 2023
I. Install Software
Tutorial sessions use the VMD - 1.9.4 alpha version (preferable), NAMD - version 2.14 (preferable), and 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). 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. Advanced users are highly encouraged to explore NAMD 3 in order to harness the enhanced speed offered in GPU-resident mode.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.
- 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)
- QwikMD Tutorial:
(pdf, 1.4M) (required tutorial files [.tar.gz, 1.1GB], [.zip, 1.1GB], individual files)
- Methods for calculaing Potentials of Mean Force (pdf, 11.1 MB) (required tutorial files [tar.gz, 106 MB])
- Parameterizing small molecules using Force Field Toolkit (ffTK) (pdf, 11.1 MB) (required tutorial files [tar.gz, 24.2 MB])
For Windows 10 users