We have performed a molecular dynamics simulation study of atactic polystyrene (a-PS) and its dimer 2,4-diphenylpentane (DPP) using a previously derived quantum chemistry based explicit atom force field. The X-ray structure factor of a-PS obtained from simulations was found to be in good agreement with experiment, reproducing the "amorphous" peak at around 1.4 Angstrom(-1) as well as the "polymerization peak" at around 0.75 Angstrom(-1) and its anomalous temperature dependence (increasing intensity with increasing temperature). We found that the amorphous peak in a-PS arises primarily from phenylphenyl correlations, with important intramolecular and intermolecular contributions. While the intermolecular component was found to shift to lower q with increasing temperature, the intramolecular component was found to be insensitive to temperature, resulting in a weak temperature dependence of the amorphous peak. Simulations revealed the presence of the polymerization peak in DPP, indicating that the designation "polymerization peak" for this feature is a misnomer. The polymerization peak in both a-PS and DPP was found to be due primarily to intermolecular correlations of backbone atoms. This underlying correlation showed the expected decrease in intensity and shifting to lower q with increasing temperature. The shifting to lower q of intermolecular phenyl-phenyl and phenyl-backbone correlations with increasing temperature was found to lead to the observed anomalous temperature dependence of the polymerization peak.