Getting started
 | This is my first attempt at a tutorial and it is actively under development. Please let me know if you encounter any problems; suggestions about modifications/additions are always welcome. |
This tutorial is designed to help users get acquainted with computational electrostatics calculations using APBS. In order to perform the provided examples, you will need:
The latest version of APBS (http://apbs.sourceforge.net) to perform the electrostatics calculations.
You will also need the following software to perform the visualizations in this tutorial. These are not required for standard APBS usage, but optionally useful for displaying results:
VMD (http://www.ks.uiuc.edu/Research/vmd/) to visualize the molecular structures and electrostatic potentials.
Gnuplot (http://www.gnuplot.info/) to plot energies, etc.
Bash (http://www.gnu.org/software/bash/bash.html) - standard on most Linux, MacOS X.
Python (http://www.python.org/) - standard on most Linux, MacOS X.
The following examples demonstrate some of the basic electrostatics which require modest computational resources; i.e., can be performed using in 0-5 min on a modern PC.
 | These examples build on one another and are designed to be carried out in order. Please read through each section completely before trying the example. |
| This tutorial require several files (linked to from the individual examples) be downloaded. It is recommended that you create a separate subdirectory (e.g., mkdir foo; cd foo) for each example. Also many browsers will display, rather than save the example files. Right-clicking on the link (or the displayed file) should present you with the option to save the file. |