Nanomedicines are typically formed by nanocarriers which can deliver in a targeted manner drugs poorly soluble in blood, increase their therapeutic activities, and reduce their side effects. Many tested nanomedicines are formed by lipids, polymers, and other amphiphilic molecules isolated or self-assembled into various complexes and micelles, functionalized nanoparticles, and other bio-compatible composite materials. Here, we show how atomistic molecular dynamics simulations can be used to characterize and optimize the structure, stability, and activity of selected nanomedicines. We discuss modeling of nanomedicines based on micelles, which can deliver selected therapeutic agents, and nanoparticles designed to act like large drugs. We show how to model nanomedicines interacting with lipid membranes, viruses, and amyloid fibrils.