GROMACS

When checking energy conservation for a pretty small system (~900atoms) for different free energy settings, I noticed that the energy conservation appears to depend on the number of cores used, and this is present for non-free-energy runs too. The attached system is a single ethanol in water, 939 atoms, and a rhombic dodecahedron box with side=2.4nm. When running with verlet kernels, reaction-field, lincs-order=3, and DLB, only simulations with a single thread appears to conserve energy, and with 8 cores the drift is horrible.

Even when limiting it to a single step and running with -reprod and -dlb no, there are large differences in forces after the first step. In this case it only appears to affect the 8-core simulation, though - the others seem to match the single-core-run. The error is present for group kernels too, and with PME (although the energy drift is smaller there, likely because the direct-space interactions are lower magnitude).

This is using the release-4-6 branch of git, and running on amd1.theophys.kth.se with acceleration enabled.