As far are good computational chemistry PhD programs go, you likely won't find a specific program for this. Instead you need to look for specific faculty, or a concentration of those faculty in a particular department. Univ. of Minnesota (Chemistry) has a number of very strong faculty. University of Illinois has a strong computational biology group (google "NAMD"). There are also great faculty at places like Princeton (chemical engineering/chemistry), Cornell.
Some other ideas...if you google "Gaussian", "GAMESS", "CPMD" or "CP2K" (these are commonly used software packages), you should turn up a bunch of research groups working with ab initio calculations or plane wave DFT.
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