FEARCF: Graph-based software library for multidimensional free energy simulations

dc.contributor.advisorNaidoo, Kevin J
dc.contributor.authorBruce-Chwatt, Tomas
dc.date.accessioned2023-03-02T08:51:49Z
dc.date.available2023-03-02T08:51:49Z
dc.date.issued2022
dc.date.updated2023-02-20T12:20:18Z
dc.description.abstractThis thesis presents the efforts to adapt the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method into the form of a software library, enabling it to be interfaced with other molecular dynamics (MD) software packages. There exist many methods to calculate the free energy of molecular systems, an important quantity when studying chemical reactions and molecular structures. One of these, FEARCF, was developed at the Scientific Computing Research Unit (SCRU). Previously, this method was restricted to usage within the CHARMM MD software package. Taking inspiration from graph theory and object-orientated design, a successful software library implementation will be demonstrated by presenting results from a range of theories including: classical, ab initio and QM/MM. Simulations are conducted for a range of systems and reaction coordinates including: water, glucose, and the GlcNAc/OGT enzyme-substrate complex.
dc.identifier.apacitationBruce-Chwatt, T. (2022). <i>FEARCF: Graph-based software library for multidimensional free energy simulations</i>. (). ,Faculty of Science ,Department of Chemistry. Retrieved from http://hdl.handle.net/11427/37119en_ZA
dc.identifier.chicagocitationBruce-Chwatt, Tomas. <i>"FEARCF: Graph-based software library for multidimensional free energy simulations."</i> ., ,Faculty of Science ,Department of Chemistry, 2022. http://hdl.handle.net/11427/37119en_ZA
dc.identifier.citationBruce-Chwatt, T. 2022. FEARCF: Graph-based software library for multidimensional free energy simulations. . ,Faculty of Science ,Department of Chemistry. http://hdl.handle.net/11427/37119en_ZA
dc.identifier.ris TY - Master Thesis AU - Bruce-Chwatt, Tomas AB - This thesis presents the efforts to adapt the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method into the form of a software library, enabling it to be interfaced with other molecular dynamics (MD) software packages. There exist many methods to calculate the free energy of molecular systems, an important quantity when studying chemical reactions and molecular structures. One of these, FEARCF, was developed at the Scientific Computing Research Unit (SCRU). Previously, this method was restricted to usage within the CHARMM MD software package. Taking inspiration from graph theory and object-orientated design, a successful software library implementation will be demonstrated by presenting results from a range of theories including: classical, ab initio and QM/MM. Simulations are conducted for a range of systems and reaction coordinates including: water, glucose, and the GlcNAc/OGT enzyme-substrate complex. DA - 2022_ DB - OpenUCT DP - University of Cape Town KW - Chemistry LK - https://open.uct.ac.za PY - 2022 T1 - FEARCF: Graph-based software library for multidimensional free energy simulations TI - FEARCF: Graph-based software library for multidimensional free energy simulations UR - http://hdl.handle.net/11427/37119 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/37119
dc.identifier.vancouvercitationBruce-Chwatt T. FEARCF: Graph-based software library for multidimensional free energy simulations. []. ,Faculty of Science ,Department of Chemistry, 2022 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/37119en_ZA
dc.language.rfc3066eng
dc.publisher.departmentDepartment of Chemistry
dc.publisher.facultyFaculty of Science
dc.subjectChemistry
dc.titleFEARCF: Graph-based software library for multidimensional free energy simulations
dc.typeMaster Thesis
dc.type.qualificationlevelMasters
dc.type.qualificationlevelMSc
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