Investigate physical properties of poly (ethylen glycol) for antibiofouling application

Abstract

In the research, we simulated a PEG in water to investigate the physical properties of PEG via interaction of PEG with water and temperature. We apply Avogadro software and VMD software to build and show a 3D structure of PEG with 9 monomers, named PEG9, in PDB format. Ubuntu code is used to change the structure of PEG from atomistic to coarse-grained beads. Some tools in GROMACS software are used to simulate 2000 PEG9 molecules at 300K in water and separated atoms, bonds and angles of PEG9. Then calculate the force field to consider the action of PEG in MARTINI parametrization. Finally, we applied some calculated tools to determine free energy of PEG9 and cross-comparison of different analysis techniques that can highlight problems. This research does not only give information about the interaction of PEG in water but also suggest the way generate a new system which is necessary for polymer simulation. Because unlike the protein we can get all information at Protein Data Bank, we have to calculate and build polymer system depend on the intuition about bioinformatics knowledge. Keyword: Hydrogel, poly (ethylene glycol), PEG9, GROMACS, antifouling.