The production simulation was performed in the NPT ensemble at 350 K and at a pressure of 1 atm for 935 ns using the Parrinello-Rahman barostat (all other simulation details are the same as for the NVT run). In order to determine when the NP structure had reached stationarity, we considered the time-evolution of the fraction of PLGA monomers found instantaneously within different regions of the NP core. This methodology has previously been used to study Pluronic and Tetronic micelles. Figure shows that these quantities become stationary at approximately 0.6 µs, implying that the internal structure of the NP has reached equilibrium at that point. Figure shows the radius of the NP (and its core alone) over time; we note these values plateau more quickly (after approximately 0.3 µs). Therefore, it is important to consider the internal structure of equilibrating micelles, rather than just their bulk size, in order to accurately quantify structural equilibration in MD simulations. The analysis presented in this manuscript was performed using only the stationary portion of the micelle trajectory, i.e., a burn-in time of 0.6 µs was used (so only the final 400 ns of the simulation trajectory was considered in the analysis). The average radius of gyration of the NP at equilibrium (9.93 ± 0.06 nm) shows good agreement with the experimentally measured diameter (20 nm) for this formulation. To understand how the polymer blocks and the peptides are distributed within the NP, we calculated the radial density of NP components (Figure (a)), as well as the analogous intrinsic density calculated using the intrinsic core-shell interface (ICSI) method for comparison (Figure ). The NP core is predominantly made up of LA and GA blocks. Surprisingly, a small nucleus of water forms close the center of the NP core during the self-assembly process in the unbiased CG MD simulation (this is indicated in Figure (a) by a peak in the water density curve (dark blue) centered at r ≈ -70 Å). In this central region, there are also peaks in the density of both PEG and EEK. The EEK peptides are found at the interface of small nucleus of water, as highlighted in the snapshot (Fig. )). To quantify the amount of each polymer species in the core of the NP, Figure (b) shows the percentage of coarse-grained beads representing the polymer species and water within the core. PLGA blocks account for 70% of the total number of beads within the hydrophobic core, with water making up 1.4%