There are many MultiDark simulations. All of them are done with the GADGET code. Table below lists parameters of the MultiDark simulations. More details are given Klypin et al. (2016). See also this page in for details of different simulations.Pasted Graphic
Dark matter halos were identified with spherical-overdensity halo finders Bound Density Maximum (BDM) and/or Robust Overdensity Calculation using K-Space Topologically Adaptive Refinement (RockStar). A short description of the halo finders is given here. BDM is described in Appedix A of Riebe et al. (2013) and for convenience is reproduced here.

RockStar and BDM halo finders were extensively studied and compared: see Behroozi et al. (2013) and Knebe et al. (2013). Both BDM and RockStar identify distinct halo and sub halos, but they use different algorithms to do it. The main difference between BDM in RockStar is in masses of sub halos with RockStar giving bigger masses. Circular velocities show much smaller differences.

There are two types of BDM catalogs that differ by the definition of the viral radius. Catalogs with filenames having capital letter V (e.g., CatshortV.0416.DAT) are for the verdensity 360*ρback (background density). Catalogs with capital letter W are for 200*ρcrit (critical density) for defining the halo boundary.
Raw particle data are written in the PMss format: The whole computational volume is split into equal-sized cubic domains with the number of domains typically 125 (5x5x5) or 512 (8x8x8). Each domain is surrounded by a buffer of width typically 2-5 Mpc. All particles in each domain plus its buffer are written into a separate file. Each domain and its immediate environment can be analyzed separately from other domains. There are different small variations of the PMss format. Those variations were implemented to speedup the reading and to make more portable the reading routines.