Simulations of the LHC collimation system have been carried out in previous years with the well known SixTrack code with collimation features. MERLIN is a C++ accelerator physics library that has been extended to perform collimation studies. The main features of the code are: its modular nature, allowing the user to easily implement new physics processes such as resistive wakefields and synchrotron radiation, improved scattering routines and the MPI protocol for parallel execution. MERLIN has been configured to use the same scattering routines as SixTrack in order to bench-mark the code for the LHC collimation system. In this paper we present a detailed comparison between MERLIN and SixTrack for optics and cleaning inefficiency calculation.