Thank you very much Shafat, the software I got my data file from is Towhee; a monte carlo simulation software. And yes, the output files shows that the energy is in Kcal/mol. I have used this software a few times to generate data for LAMMPS for previous works and there was no problem, although those were small molecules. So how does one remedy this “excessive forces”? Axel has suggested I do a minimization, which I am going to do right away.