A constraint condition generating apparatus generates a constraint condition which should be output to a molecular dynamics simulator for simulating a behavior of a molecule based on a molecular dynamics method under the constraint condition for freezing a part of the degree of freedom within the molecule. This apparatus comprises bond constraint condition setting and releasing unit for setting a bond constraint list comprising the number of two atoms whose bond are to be constrained and a bonding distance between two atoms, and for releasing the constraint of the bond of two atoms, angle constraint condition setting and releasing means for setting an angle constraint condition including a bonding distance between two atoms which are not common and for releasing a part of angle constraint condition in accordance with a designation by a user; and a torsion constraint condition setting and releasing unit for setting a torsion constraint condition including a bonding distance between two atoms which are not common, and for releasing a part of a constraint condition in accordance with a designation by a user.