Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial

This article describes the development, implementation, and use of web-based lessons'' to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e. g., phones and tablets), allowing easy integration of these advanced simulation techniques into course-work. Finally, one of the primary objections to web-based systems like CHARMMing has been that point and click'' simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.