The aim of the study was to analyse where different organic molecules situated themselves in relation to the water surface of a water microdroplet and use the resulting data to compare three different forcefields in the simulation package GROMACS. The forcefields used were: General AMBER forcefield (GAFF), Optimized potentials for liquid simulations - all atoms (OPLS-AA), and CHARMM general force field (CGenFF). A library of 146 molecules were simulated using molecular dynamics. Out of the 146 molecules only 65 resulted in useful data for the comparison of the forcefields. The molecules were placed in the centre of a water microdroplet and their movements were simulated for a duration of 1 ns. The trajectories and positions of the molecules were stored and from each simulation a density profile was generated, showing where the molecules situated themselves. The distance from the peak of the density profile to the water surface was calculated and compared between the different forcefields. To analyse the data further some of the molecules were divided into subsets based on their functional groups to see if any trends were visible. Although inconclusive, the data suggested that different forcefields were more or less agreeable depending on the functional group of the molecules, for example OPLS-AA differed from CGenFF and GAFF in the case of alcohols.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:uu-415316 |
| Date | January 2020 |
| Creators | Sawert, David, Anderhagen Holmes, Oskar, Johanson, Aron |
| Publisher | Uppsala universitet, Molekyl- och kondenserade materiens fysik, Uppsala universitet, Molekyl- och kondenserade materiens fysik, Uppsala universitet, Molekyl- och kondenserade materiens fysik |
| Source Sets | DiVA Archive at Upsalla University |
| Language | Swedish |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | MATVET-F |
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