Are the CUDA libraries in the library search path (controlled at the system level by /etc/ld.so.conf and friends and at the user level by the LD_LIBRARY_PATH environment variable)?
Edit to add: There are several bugs in the DOMDEC_GPU code in c40a1. Since you've got access to alpha releases, you should in principle be using c40a2 or, as Lennart suggested, OpenMM.
Edit a second time: Using the gpu machine type is not really suggested at this point AFAIK; instead you should be using DOMDEC_GPU (see domdec.doc) with the caveat given above or OpenMM. Obviously my reading comprehension level is going downhill and I should be getting to bed soon :-).
Last edited by tim; 03/20/15 02:24 AM.