In recent years an engineered form of discoloidal high-density lipoprotein particle, called nanodisc, has been proposed as a platform to study membrane proteins. A nanodisc is a non-covalent assembly of phospholipids and two membrane scaffold proteins which wrap around the bilayer, shielding the phospholipids’ hydrophobic alkyl chains from the aqueous environment. During the reconstitution process a membrane protein is simultaneously assembled into the nanodisc core. The nanodisc forms a soluble lipid bilayer that enables membrane protein function and stability in solution while also preventing unwanted aggregation.In this work we present an automated method for building arbitrary nanodiscs and example applications to membrane proteins from different families. We use the MARTINI coarse-grained (CG) force field with the elastic network model ELNEDYN to generate initial configurations of membrane protein-loaded nanodiscs, where the size and composition of the system is fully controlled. The system can be studied using either CG molecular dynamics simulations to analyze properties like lipid mixing and packing in the nanodiscs, or backmapped after equilibration to an atomistic resolution for more detailed analyses.