Dear Petr,
Your question about van der Waals (vdW) interactions is not clearly formulated. In general, vdW interactions are defined between all non-bonded species, as opposite to chemically bonded species in, e.g., molecules. And the standard way for vdW interaction lists since 1967 is the Verlet method (Verlet list). Application of non-bonded interactions to atomic species in the same molecule are subject to special artificial ‘rules’, and are force-field (FF) dependant. Empirical FF are basically many-dimensional fits of the potential energy in the respective hyperspaces, and there is little physics in this procedure, but rather art and convenience. The reason for various treatments of ‘1-4’ interactions is the differences in developer preferences, the way how they see of how much of ‘non-bonded’ contribution should be mixed with ‘chemistry’. One cannot double count the same interaction, even under the different guises. The ‘1-2’, ‘1-3’, and ‘1-4’ lists are usually handled by different means from vdW interactions, and have meaning only when the system contains ‘molecules’. So, to answer your question, if there are no dihedrals in the system (e.g., only molecules with no more than 3 atoms), then there are no ‘1-4’ terms, and there is no scaling problem. Simple.
In DL_POLY 4 (or 5) and DL_POLY Classic there are different strategies for vdW interactions: DLP_Classic uses Verlet list, while DL_POLY 4 and above uses spatial (domain) decomposition – completely different strategy.
Hope this helps,
Vlad