Dear @ArghyaC,
You can run your simulation without using the GCR-SPE (and therefore the atmospheric layers) by sampling directly from the *.spc files: that would require some cautions. Note also that the *.spc files have log energy bins and the spectra range over many orders of magnitude.
With regard to the sampling, you can refer to the following post on the forum: Sampling from energy spectra
The tool provided by Chris can be used to sample from the *.spc files, but you should pay attention to the high energy tail in your energy-spectra, since normally this has a non-negligible contribution. Depending on your specific application, and since you are not going to simulate the full transport through the atmosphere layers, you may need to apply a certain bias to the high-energy bins.
I will suggest to carefully read the README file included with the tool, since there are different sampling techniques you can use.
Hope that this can be a useful starting point for your simulation.
Cheers,
Angelo