Magnetic nanoparticles (MNPs) can organize into novel structures in solutions with excellent order and unique geometries. However, studies of the self-assembly of smaller MNPs are challenging due to a complicated interplay between external magnetic fields and van der Waals, electrostatic, dipolar, steric, and hydrodynamic interactions. Here, we present a novel all-atom molecular dynamics (AMD) simulation method to enable detailed studies of the dynamics, self-assembly, structure and properties of MNPs as a function of core sizes and shapes, ligand chemistry, solvent properties, and external field. We demonstrate the use and effectiveness of the model by simulating the self-assembly of oleic acid ligand-functionalized magnetite (Fe3O4) nanoparticles, with spherical and cubic shapes, into rings, lines, chains, and clusters under a uniform external magnetic field. We found that the long-range electrostatic interactions can favor the formation of a chain over a ring, the ligands promote MNP cluster growth, and the solvent can reduce the rotational diffusion of the MNPs. The presence of ligands promotes the growth of particle aggregate due to increased hydrophobic interaction. The methods and simulation protocol developed in this work applies to a wide range of nanoparticle synthesis, aggregation and manipulation studies where ligand, solvent composition, and magnetic interaction play a significant role.