Optimization of force fields for molecular dynamics

dc.contributor.advisorElber, Ron
dc.creatorDi Pierro, Micheleen
dc.date.accessioned2015-02-09T18:08:14Zen
dc.date.issued2014-12en
dc.date.submittedDecember 2014en
dc.date.updated2015-02-09T18:08:15Zen
dc.descriptiontexten
dc.description.abstractA technology for optimization of potential parameters from condensed phase simulations (POP) is discussed and illustrated. It is based on direct calculations of the derivatives of macroscopic observables with respect to the potential parameters. The derivatives are used in a local minimization scheme, comparing simulated and experimental data. In particular, we show that the Newton Trust-Region protocol allows for accurate and robust optimization. POP is illustrated for a toy problem of alanine dipeptide and is applied to folding of the peptide WAAAH. The helix fraction is highly sensitive to the potential parameters while the slope of the melting curve is not. The sensitivity variations make it difficult to satisfy both observations simultaneously. We conjecture that there is no set of parameters that reproduces experimental melting curves of short peptides that are modeled with the usual functional form of a force field. We then apply the newly developed technology to study the liquid mixture of tert-butanol and water. We are able to obtain, after 4 iterations, the correct phase behavior and accurately predict the value of the Kirkwood Buff (KB) integrals. We further illustrate that a potential that is determined solely by KB information, or the pair correlation function, is not necessarily unique.en
dc.description.departmentComputational Science, Engineering, and Mathematicsen
dc.format.mimetypeapplication/pdfen
dc.identifier.urihttp://hdl.handle.net/2152/28355en
dc.language.isoenen
dc.subjectMolecular dynamicsen
dc.subjectOptimizationen
dc.subjectForce fielden
dc.subjectPeptideen
dc.subjectTert-butanolen
dc.subjectButyl alcoholen
dc.subjectTert-butylen
dc.subjectParameters refinementen
dc.subjectMolecular mechanicsen
dc.subjectMelting curveen
dc.subjectNewton Methoden
dc.subjectSimulationen
dc.subjectBiophysicsen
dc.subjectKirkwood-Buffen
dc.subjectTrust regionen
dc.titleOptimization of force fields for molecular dynamicsen
dc.typeThesisen
thesis.degree.departmentComputational Science, Engineering, and Mathematicsen
thesis.degree.disciplineComputational and Applied Mathematicsen
thesis.degree.grantorThe University of Texas at Austinen
thesis.degree.levelDoctoralen
thesis.degree.nameDoctor of Philosophyen

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