Hi Peter,
The real problem is that it's creating water molecules that are very tightly packed together in a very high energy configuration, and the simulation is blowing up.
yes, this sorted it out. Phew
I guess the issue is numerical round-off. When I find the time, I'll see if I get the same problem with the double-precision version of OpenMM. I expect the problems we have been experiencing in our other simulations then also have to do with the spacing of the atoms. We are using OpenMM to speed up a CPU-based MD library which runs in double precision and I suspect this is where most of the issues arise from, as we pass the initial simulation settings, generated in this library, to OpenMM. It's good to know where to look...
BTW, just for the record, with the correction you suggested, I managed to run a 70x70x70 water box in the HelloWaterBox example on a 2GB Quadro 4000. Not bad!
Thank you for your help!
Spela