fixed incorrect virial and pressure averages

fixed incorrect virial and pressure averages

Removed a second, incorrect setting of flags for storage of energy averages
in mdrun.
This would cause incorrect averages of the virial and pressure to be stored
in the energy file and printed at the end of the log file when the lowest
common denominator of nstcomm, nsttcouple and/or nstpcouple was less than
nstcalcenergy. Note that the instantaneous values and the actual simulation
results were all correct.
Additionally there was a potential issue with parallel checkpoint signalling
with -gcom larger than nstlist which could lead to hanging of mdrun.
This fixes #696