We present the results of modeling and simulating the Hamamatsu R5912 photomultiplier tube that is used in most of the sites of the Latin American Giant Observatory (LAGO). The model was compared with data of in-operation water Cherenkov detectors (WCD) installed at Bucaramanga-Colombia and Bariloche-Argentina. The LAGO project is an international experiment that spans across Latin America at different altitudes joining more than 35 institutions of 11 countries. It is mainly oriented to basic research on gamma-ray bursts and space weather phenomena. The LAGO network consists of single or small arrays of WCDs composed mainly by a photomultiplier tube and a readout electronics that acquires single-particle or extensive air shower events triggered by the interaction of cosmic rays with the Earth atmosphere.