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Molecular Dynamics Simulations Utilizing the GPU

  • Molecular dynamics (MD) as a field of molecular modelling has great potential to revolutionize our knowledge and understanding of complex macromolecular structures. Its field of application is huge, reaching from computational chemistry and biology over material sciences to computer-aided drug design. This thesis on one hand provides insights into the underlying physical concepts of molecular dynamics simulations and how they are applied in the MD algorithm, and also briefly illustrates different approaches, as for instance the molecular mechanics and molecular quantum mechanics approaches. On the other hand an own all-atom MD algorithm is implemented utilizing and simplifying a version of the molecular mechanics based AMBER force field published by \big[\cite{cornell1995second}\big]. This simulation algorithm is then used to show by the example of oxytocin how individual energy terms of a force field function. As a result it has been observed, that applying the bond stretch forces alone caused the molecule to be compacted first in certain regions and then as a whole, and that with adding more energy terms the molecule got to move with increasing flexibility.

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Author:Christina Krieg
Referee:Stefan Müller, Bastian Krayer
Document Type:Bachelor Thesis
Date of completion:2020/02/14
Date of publication:2020/03/05
Publishing institution:Universität Koblenz, Universitätsbibliothek
Granting institution:Universität Koblenz, Fachbereich 4
Release Date:2020/03/05
Number of pages:i, 38
Institutes:Fachbereich 4 / Institut für Computervisualistik
Licence (German):License LogoEs gilt das deutsche Urheberrecht: § 53 UrhG