I’m not sure if I understand your question. Are you asking why we use the EAM potential? The EAM potential achieves more accurate results than many other formalisms by fitting parameters to experimental results for individual elements or compounds. For bulk material simulations it is not enough to simply apply a LJ potential, and it is too computationally expensive to use the full quantum description as in LAPW simulations.
It is possible to calculate the phonon dispersion curve by generating the Dynamical Matrix, which is a function of the basis atom’s interaction with surrounding atoms coupled with the phonon wave vector.
If you’d like more information on what I’m doing I suggest you read these papers:
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TVW-46TY3RB-15P&_user=650615&_coverDate=11/30/1985&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1367062130&_rerunOrigin=google&_acct=C000035118&_version=1&_urlVersion=0&_userid=650615&md5=4e3ead08c753b5422a54d9772e66c142
-AdamC