GOMC NVT and NPT simulations halt with error if two boxes are specified

[jpotoff]

The current default behavior if for GOMC to terminate with an error if the user specifies two simulation boxes as input. Perhaps it would be better to have GOMC print a warning that it was ignoring the second set of input files and continue to run?

[LSchwiebert]

I guess there are two ways to look at it. Specifying two simulation boxes for an NVT or NPT simulation might be a mistake. We could consider issuing a warning message and running in expert mode.

If you think that a user wouldn't specify NVT or NPT instead of GEMC by mistake, and just have the extra box by mistake, then we can make the change. It's an easy patch. Just considering the options.