| 摘要 |
The present invention provides a constrained stochastic dynamical method for simulating the motion of a molecular system. The method simulates the motions of atoms within the molecular system by evaluating first order force expressions for all the atoms over a series of time steps. The force expressions include terms for frictional forces, non-covalently interatomic forces, thermal noise forces, and covalent constraining forces. Relatively long time steps can be used because the fast motions (such as vibrations associated with covalent bonds) are not explicitly considered. Rather, the fast molecular motions associated with covalent bonds are averaged around their equilibrium bond lengths and, in some cases, bond angles. This is implemented by introducing (1) thermal noise forces, and (2) constraining forces fixing the relative positions of some atoms based upon their covalent bonds. Because the method treats the movement of atoms within a molecular system as overdamped, the atomic force balances are first order force expressions which can be evaluated without iteration.
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