Computational Biophysics Workshop - Pittsburgh, October 12 - 15, 2020

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.

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.

Note: participants may also download and get assistance with other tutorials from the TCBG tutorials website during the workshop.

For Windows 10 users

  • You can add the directory of NAMD binary into the system path variable so we can skip the lengthy directory name when executing namd2, here is a step-by-step guide

  • Variables in Windows cmd appear as %var% instead of $var, so the path can be %USERPROFILE%\NAMD_2.14_Win64-multicore-CUDA (similar to $HOME/NAMD_2.14_Win64-multicore-CUDA in bash)

  • Similarly, one can also add "C:\Program Files (x86)\University of Illinois\VMD" to the path variable so that vmd can be called directly from the cmd interface without going through the start menu

  • Executing "namd2 input.conf > output.log &" will not return to the command-line interface with the program running in the background. To execute a program in the background under Windows cmd, do "start /B namd2 input.conf > output.log" (effectively this creates a subshell in the background to execute the following command, so the parent cmd interface cannot be terminated until the subshell command is completed).

  • While WordPad need to be executed from the start menu, notepad can be directly called from cmd without specifying path (the binary exe is in Windows/System32 so it can be run from everywhere)

  • (Optional) If user prefers the un*x command interface but has to use a windows machine, they can use the Windows subsystem for Linux, installation guide. Note that currently the subsystem doesn't directly support a GUI yet, so VMD is not working properly. The file system of the linux-subsystem appears to be independent of the windows C:\ drive however it's actually a hidden directory under the windows user's home. See details