I want to run wp_query on a separate php file for an ajax call

Question

For example:

Answer 1

You have to include the file that has the Wordpress functions located on the main directory of the Wordpress Installation:

define('WP_USE_THEMES', false);  
require_once('../../../wp-load.php');

../../../ = path to the main directory on your installation

I found a nice tutorial about this here.