The molecular structure of poly(amido amine) dendrimers is investigated with molecular dynamics simulations using the Amber 7 modeling package. A method for defining residues for complex molecules is developed, and it enables the study of the effects of protonation of the primary and tertiary amines. The effects of implicit solvents versus explicit solvents as well as the pH of the solution on the molecular structure are calculated. Good agreement with experimental results for the radius of gyration measured in methanol by X-ray scattering is observed for simulations with an explicit solvent and protonation of the primary amines. Calculations of the intramolecular atomistic pair correlation function show a dense core, as well as the presence of voids filled with the solvent inside the molecule. The primary amines (end groups) are shown to access the molecular interior by backfolding. Comparisons with experiments and other reported simulation results highlight the advantages of the approach developed here. (c) 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 3062-3077,2006.