The Latin American Giant Observatory (LAGO) is an observatory spanning over Latin America in a wide range of latitudes with different rigidity cut offs and atmospheric depths.The motivation of the Observatory is to study, using Water Cherenkov Detectors (WCD), the atmospheric radiation and the space weather through the measurement of secondary particles produced during the interaction of astroparticles with the atmosphere. Here, we present the methodology for estimating the number of Cherenkov photons detected by the photo-multiplier tube in a WCD in any geographical position. To do this, the secondary particle flux of cosmic rays is calculated and a geomagnetic field correction is applied. The CORSIKA and MAGCOS programs are used. In addition, the outcome of the simulation is used as an input to the Geant4 program in order to mimic the response of the detector. As a result, the distribution of photo-electrons is obtained for the total particle flux, where its behavior resembles the characteristic signals of this kind of detector and could be used to calibrate the system.This methodology was applied for five LAGO detector sites, located at different latitudes and altitudes above sea level, between Chile and Mexico.