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Molecular Dynamics and the Water Molecule: An Introduction to Molecular Dynamics for Physical Chemistry Students
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Abstract
A general approach to Molecular Dynamics procedures (MD), that can be included as a lesson in different parts of a physical chemistry program, is presented. The basic idea that a MD calculation consists on analyzing the evolution with time of the studied sample is presented and the difficulties arising from the amount of data to be analyzed and the computation of atomic coordinates are explained. Newton's equation of motion is integrated for a trivial system formed by just one isolated particle. Next, a system of two interacting particles is used to illustrate the leap frog algorithm employed for the integration in more realistic cases. Finally, the results obtained by performing a real MD calculation on the water molecule are presented, explained and compared with some basic ideas that we all have about this molecule.
Keywords (Audience):
Upper-Division UndergraduateKeywords (Domain):
Physical ChemistryKeywords (Pedagogy):
Computer-Based LearningKeywords (Subject):
Molecular ModelingCiting Articles
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- Received: August 03, 2009
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