The Latin American Giant Observatory (LAGO) is an extensive network of water Cherenkov detectors spread across Latin America, functioning as an astroparticle observatory. With its broad range of altitudes and geomagnetic rigidity cut-offs, the primary focus of LAGO's scientific program is to study space weather, climate phenomena, and high-energy astrophysical transients from ground level. To bolster these programs, the comprehensive simulation framework of ARTI and onedataSim was developed. This framework enables the calculation of the total secondary particle flux and the corresponding signals expected in various types of detectors operating anywhere in the world. It also incorporates the effects of real-time atmospheric and geomagnetic conditions, both secular and disturbed. These tools harness the expanding computational capabilities of high-performance computing facilities and cloud-based computing environments. By integrating these tools and infrastructures, we have managed to extend the total integration times of the background flux and the energy range of atmospheric neutrons. In this contribution, we illustrate how this intricate simulation sequence aids in achieving LAGO's scientific objectives. We also explore other applications, such as estimating the expected dose on board commercial flights, simulating the muon flux for muography studies, determining the distribution of neutrons in nuclear and medical facilities, and estimating the rate of errors produced by atmospheric neutrons in the upcoming generation of exascale supercomputing centers worldwide.