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Dipeptide Structure and Dynamics

Adam, Ahmad Y. (2008) Dipeptide Structure and Dynamics. Master's Thesis, University of Pittsburgh. (Unpublished)

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Classical mechanical calculations have been performed to minimize the structure of alanine dipeptide using different Amber force fields. The minimization process leads to the second lowest conformer, the C5 conformer, compared to ab initio methods and experiment which identify the C7eq conformer as the lowest energy conformer. Then, a classical molecular dynamics calculation was done to search for the structure of the C7eq conformer. Starting from the C5 conformer, the structure of the C7eq conformer was identified after 28 ps of the simulation process. Possible reasons for this behavior are discussed.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Adam, Ahmad
Date: 26 September 2008
Date Type: Completion
Defense Date: 7 August 2008
Approval Date: 26 September 2008
Submission Date: 5 August 2008
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Institution: University of Pittsburgh
Schools and Programs: Dietrich School of Arts and Sciences > Chemistry
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: alanine dipeptide; force fields; molecular dynamics
Other ID:, etd-08052008-214503
Date Deposited: 10 Nov 2011 19:57
Last Modified: 15 Nov 2016 13:48


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