Methodological considerations on molecular dynamics simulations of DNA oligonucleotides

Methodological aspects of solvent effects, simulation protocol, analysis and visualization of results, accuracy, and sensitivity of results to force field parametrization are discussed for molecular dynamics simulation on oligonucleotides. Recent results comparing AMBER, CHARMM and GROMOS force fields are included. The calculation of build‐up curves for the nuclear Overhauser effect from simulations is also described.