Initialize inputrec better in genbox

Incoming NBNXN patches change the behaviour if you just leave the VDW
modifier set to zero. The modifier is not supposed to be zero, because
grompp is supposed to change eintmodPOTSHIFT_VERLET to something
non-zero, but since we don't have a vanilla constructor for an
inputrec and use it outside grompp, we have a horrible flow-on effect.

So we set both the modifiers explicitly, to avoid these problems.

Change-Id: I2f8381e81104e673fb1a602b2d9cac1ccd81fff0