Text S1 - Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations

This file contains supporting methods; detailed description of supporting methods, algorithms and limitations. Molecular dynamics simulations details, equilibration and mutation of the nucleosome models, mutations and thermodynamic integration method. Description of free energy calculation limitations, trajectory analysis, mesoscopic model of nucleosome deformation energy algorithm, mesoscopic model limitations rotational positioning and phase calculation. The supporting Tables S1, S2, S3 and the supporting Figures S1, S2, S3, S4, S5, S6, S7. (DOCX)