eprintid: 8912
rev_number: 3
userid: 6
dir: disk0/00/00/89/12
datestamp: 2011-11-10 19:57:23
lastmod: 2016-11-15 13:48:16
status_changed: 2011-11-10 19:57:23
type: thesis_degree
metadata_visibility: show
contact_email: aadam@vt.edu
item_issues_count: 0
eprint_status: archive
creators_name: Adam, Ahmad Y.
creators_email: aadam@vt.edu
title: Dipeptide Structure and Dynamics
ispublished: unpub
divisions: sch_as_chemistry
full_text_status: public
keywords:  alanine dipeptide; force fields; molecular dynamics
abstract: 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.
date: 2008-09-26
date_type: completed
institution: University of Pittsburgh
refereed: TRUE
etd_defense_date: 2008-08-07
etd_approval_date: 2008-09-26
etd_submission_date: 2008-08-05
etd_access_restriction: immediate
etd_patent_pending: FALSE
assigned_doi: doi:10.5195/pitt.etd.2011.8912
thesis_type: thesis
degree: MS
committee: David Pratt (pratt@pitt.edu) - Committee Chair
committee: Peter Siska (pes@pitt.edu) - Committee Member
committee: Stephane Petoud (spetoud@pitt.edu) - Committee Member
etdurn: etd-08052008-214503
other_id: http://etd.library.pitt.edu/ETD/available/etd-08052008-214503/
other_id: etd-08052008-214503
citation:   Adam, Ahmad Y.  (2008) Dipeptide Structure and Dynamics.  Master's Thesis, University of Pittsburgh.    (Unpublished)  
document_url: http://d-scholarship-dev.library.pitt.edu/8912/1/MSAugust08.pdf