Parametrization of Interactions in DNA Complexes for Molecular Dynamics Simulation

DNA condensation plays a crucial role in cellular processes such as gene expression, replication, and chromatin organization. This study focuses on refining the OxDNA coarse-grained model by parametrizing its interactions with DNA using an All-Atoms model as a reference, specifically in the presence of the condensing agent Cobalt(III) Hexammine. Our approach involves systematically adjusting the sigma (diameter) values of DNA's base and sugar components to optimize the OxDNA model, ensuring it accurately represents molecular forces and interaction energies. By constructing 3D matrices to store the energy values, we compare Van der Waals and electrostatic interactions between the two models, assessing discrepancies through the resulting coefficient of difference. Preliminary results highlight the impact of sigma values on model accuracy, with optimal parameters identified within specific base and sugar sigma ranges. Future work will explore additional orientations, charge considerations, and force-based comparisons to enhance the fidelity of the coarse-grained model for molecular dynamics simulations of DNA condensation.