1. A method of simulating the conformations of a molecular system with the aid of a computer system, the molecular system having a plurality of atoms partially limited in their ability to move with respect to one another by constraining forces and frictional forces, the method comprising the following steps: (a) inputting into the computer system a computer usable representation of the molecular system, the representation having an arrangement of atoms determined, in part, by the constraining forces, the representation also having degrees of freedom; (b) determining the interatomic non-bonding forces acting on each atom of the representation, the interatomic non-bonding forces acting on each atom caused by the other atoms in the molecular system; (c) obtaining a total non-frictional force on the atoms by (i) combining thermal noise forces with the interatomic non-bonding forces acting on each atom, and (ii) projecting out of said interatomic non-bonding forces and noise forces, those force components in the directions of the constraining forces in the molecular system such that the atoms of the representation are constrained to their positions with respect to other atoms in the direction of the constraining forces; and (d) moving the atoms of the representation into a new conformation as determined by an overdamped Langevin dynamics description of the forces acting on the atoms, the overdamped Langevin description including the total nonfrictional forces and the frictional forces, wherein movement of the atoms is used to determine one or more specified properties of the molecular system.