Fixing a problem when dhdl and replex are not multiples

Problems is fixed by guaranteeing the free energy information
is now updated at a frequency that is the greatest common
denominator of the relevant internal variables.

An existing gcd function was taken from gmx_genion and put
in the include/maths.h file.

Change-Id: I7473185ab02c7c9a7557fbaa165bb20b63bafb7a