University of Natural Resources and Life Sciences, Vienna (BOKU) - Research portal

Logo BOKU Resarch Portal

Gewählte Master / Diploma Thesis:

Daniel Fast (2016): Solvation free energies of amino acid analogues using molecular dynamics simulations.
Master / Diploma Thesis - Institut für Molekulare Modellierung und Simulation (MMS), BOKU-Universität für Bodenkultur, pp 52. UB BOKU obvsg

Data Source: ZID Abstracts
Abstract:
The free energy can be seen as the driving force of all molecular processes. Molecular dynamics simulations are a valuable tool for predicting free energy changes in the context of ligands binding to proteins or solvating small molecules. A reference method for such calculations is the accurate but inefficient thermodynamic integration (TI), which requires the simulation of a large number of unphysical intermediate states. In the present thesis, various approaches for computing the solvation free energies of amino acid analogues are investigated. In order to evaluate more efficient methods, the polar and apolar contributions to the solvation free energies are determined separately. With respect to the TI reference results, the combination of third power fitting (TPF) and one-step perturbation (OSP) delivers quite accurate solvation free energies. At the same time, the TPF/OSP approach is efficient and capable of reproducing experimental data.

Beurteilende(r): Oostenbrink Chris
1.Mitwirkender: Setz Martina

© BOKU Wien Imprint