Fix all cppcheck warnings

Fix all cppcheck warnings

All warnings were style issues no bugs. All issues resolved (1.53).
cppcheck can be run without suppressions and doesn't produce any
warnigns.

To run (from src folder):
cppcheck -j4 --enable=style */*.cpp */*/*.cpp */*/*/*cpp \
   -DHAVE_CONFIG_H -D CPPCHECK -I gromacs/legacyheaders/

Change-Id: I2da1c824a1798e6773520de59470f7488fff738c