move 4.6beta1 to 4.6 and make it work as such, too

Signed-off-by: Fotis Georgatos <fotis.georgatos@uni.lu>
promote FFTW 3.3.1 to 3.3.3 for GROMACS and fix dependency bug

Signed-off-by: Fotis Georgatos <fotis.georgatos@uni.lu>