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Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

ABSTRACT: 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 coursework. 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.

SUBMITTER: Miller BT

PROVIDER: S-EPMC4109840 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

Miller Benjamin T BT Singh Rishi P RP Schalk Vinushka V Pevzner Yuri Y Sun Jingjun J Miller Carrie S CS Boresch Stefan S Ichiye Toshiko T Brooks Bernard R BR Woodcock H Lee HL

PLoS computational biology 20140724 7

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 adde ...[more]

PMID: 25057988

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Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

Publications

Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

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