ALGORITHMS FOR MACROMOLECULAR DYNAMICS AND CONSTRAINT DYNAMICS
ALGORITHMS FOR MACROMOLECULAR DYNAMICS AND CONSTRAINT DYNAMICS
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DOI：
10.1080/00268977700102571
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发表时间：
1977-01-01
影响因子：
1.7
通讯作者：
BERENDSEN, HJC
中科院分区：
文献类型：
--
作者：
VANGUNSTEREN, WF;BERENDSEN, HJC
研究了分子动力学的计算机模拟方法在高分子中的应用。蛋白质胰蛋白酶抑制剂（BPTI），由454个联合原子组成，被用作一个例子。不同的算法集成的运动方程进行了比较，在理论上和实践中。研究了大分子链结构在多大程度上允许通过在链动力学中引入约束来减少计算量，提出了一种计算方案，通过该方案可以将约束引入预测-校正算法中.算法的最佳选择取决于所需的解的精度和作用在分子上的力的特性，即这些力是否有噪声。对于非约束动力学的齿轮预测校正算法产生最好的结果，而约束动力学的齿轮和Verlet算法产生可比的结果。键长约束的应用减少了所需的计算机时间的一个因素3。不建议包含焊接角约束。
The application of the computer simulation method of molecular dynamics to macromolecules is investigated. The protein trypsin inhibitor (BPTI), consisting of 454 united atoms, is used as an example. Different algorithms for integrating the equations of motion are compared, both theoretically and in practice. It is examined to what extent the chain structure of a macromolecule allows a reduction of the computational effort by the introduction of constraints in the dynamics of the chain.A calculational scheme is proposed, by which constraints can be incorporated in predictor-corrector algorithms. The optimum choice of an algorithm depends on the desired accuracy of the solution and on the character of the forces acting on the molecule, viz. whether these are noisy or not. For nonconstraint dynamics a Gear predictor-corrector algorithm yields the best results, whereas for constraint dynamics the Gear and Verlet algorithms produce comparable results. The application of bond-length constraints reduces the required computer time by a factor of 3. The inclusion of bondangle constraints is not recommended.