A MODIFIED SHAKE ALGORITHM FOR MAINTAINING RIGID BONDS IN MOLECULAR-DYNAMICS SIMULATIONS OF LARGE MOLECULES
A MODIFIED SHAKE ALGORITHM FOR MAINTAINING RIGID BONDS IN MOLECULAR-DYNAMICS SIMULATIONS OF LARGE MOLECULES
复制标题
DOI：
10.1016/0021-9991(89)90160-5
复制
发表时间：
1989-12-01
影响因子：
4.1
通讯作者：
NAGUMO, M
中科院分区：
文献类型：
--
作者：
LAMBRAKOS, SG;BORIS, JP;NAGUMO, M
我们提出了一个新的修改的SHAKE算法，MSHAKE，保持固定的距离在分子动力学模拟的多原子分子。MSHAKE算法通过修改蛙跳算法以包括约束力来应用，计算约束力的初始估计，然后迭代地校正维持固定距离所需的约束力。因此，MSHAKE应该总是比SHAKE更快地收敛。此外，每个时间步约束力的显式确定使得MSHAKE方便用于分子动力学模拟，其中键应力是一个重要的动力学量。
We present a new modification of the SHAKE algorithm, MSHAKE, that maintains fixed distances in molecular dynamics simulations of polyatomic molecules. The MSHAKE algorithm, which is applied by modifying the leapfrog algorithm to include forces of constraint, computes an initial estimate of constraint forces, then iteratively corrects the constraint forces required to maintain the fixed distances. Thus MSHAKE should always converge more rapidly than SHAKE. Further, the explicit determination of the constraint forces at each timestep makes MSHAKE convenient for use in molecular dynamics simulations where bond stress is a significant dynamical quantity.