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FEARCF: Graph-based software library for multidimensional free energy simulations
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 molecula...
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| Format: | Thesis |
| Language: | English |
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Department of Chemistry
2023
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| _version_ | 1867613893594972161 |
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| access_status_str | Open Access |
| author | Bruce-Chwatt, Tomas |
| author2 | Naidoo, Kevin J |
| author_browse | Bruce-Chwatt, Tomas Naidoo, Kevin J |
| author_facet | Naidoo, Kevin J Bruce-Chwatt, Tomas |
| author_sort | Bruce-Chwatt, Tomas |
| collection | Thesis |
| description | 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. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/37119 |
| institution | University of Cape Town (South Africa) |
| language | eng |
| last_indexed | 2026-06-10T12:43:23.285Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Department of Chemistry |
| publisherStr | Department of Chemistry |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/37119 FEARCF: Graph-based software library for multidimensional free energy simulations Bruce-Chwatt, Tomas Naidoo, Kevin J Chemistry 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. 2023-03-02T08:51:49Z 2023-03-02T08:51:49Z 2022 2023-02-20T12:20:18Z Master Thesis Masters MSc http://hdl.handle.net/11427/37119 eng application/pdf Department of Chemistry Faculty of Science |
| spellingShingle | Chemistry Bruce-Chwatt, Tomas FEARCF: Graph-based software library for multidimensional free energy simulations |
| thesis_degree_str | Master's |
| title | FEARCF: Graph-based software library for multidimensional free energy simulations |
| title_full | FEARCF: Graph-based software library for multidimensional free energy simulations |
| title_fullStr | FEARCF: Graph-based software library for multidimensional free energy simulations |
| title_full_unstemmed | FEARCF: Graph-based software library for multidimensional free energy simulations |
| title_short | FEARCF: Graph-based software library for multidimensional free energy simulations |
| title_sort | fearcf graph based software library for multidimensional free energy simulations |
| topic | Chemistry |
| url | http://hdl.handle.net/11427/37119 |
| work_keys_str_mv | AT brucechwatttomas fearcfgraphbasedsoftwarelibraryformultidimensionalfreeenergysimulations |