1999 Honda Civic Noises from 1999 honda civic

My 1999 honda civic has recently start making a weird noise while I am driving. When I press the accelerator pedal and speed reaches between 40 and 60 miles per hour, the engine start making a weird noise. Also when I drop my speed down between 40 and 60 miles per hour it makes the same sound again. The noise sounds like metal grinding and it happens when I hit gear 2 to gear 3. But when I put my car in neutral and drop my speed between 40 and 60, it didn't make any noise. I would like to know what happen to my car. Thanks