We describe a new pipeline for computing non-bonded forces and its integration into the Proto- Mol molecular dynamics (MD) code. There are sev- eral innovations: a novel interpolation strategy, includ- ing use of higher order terms; coe?cient generation with orthonormal functions; the introduction of \semi- foating point" numbering; and various issues related to system integration. As a result, we are able to model far more particle types, without relying on complex bu?ering, and obtain higher accuracy than previously. A two pipeline accelerator has been implemented on a 2004-era Xilinx VirtexII Pro VP70, integrated into ProtoMol, and tested with an enzyme inhibitor model having 8000 particles and 26 particle types. Despite performing all O(n) work on the host PC, as well as the data conversion and communication overhead, this implementation yields 5:5? to 15:7? speed-ups over a 2.8GHz PC (depending on whether cell lists are used), and with accuracy comparable to the serial code.