An assessment of optimal time scale of conformational resampling for parallel cascade selection molecular dynamics
An assessment of optimal time scale of conformational resampling for parallel cascade selection molecular dynamics
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DOI：
10.1080/08927022.2017.1362696
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发表时间：
2018-01-01
影响因子：
2.1
通讯作者：
Shigeta, Yasuteru
中科院分区：
文献类型：
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作者：
Harada, Ryuhei;Shigeta, Yasuteru
平行级联选择分子动力学（PaCS-MD）已被提出作为一种构象采样方法，用于通过重复循环的短时MD模拟来增强从给定反应物到产物的结构转变。在本文中，我们评估了如何通过改变模拟长度的时间尺度的短时间MD模拟影响的计算效率。总之，ps阶（t（ps））PaCS-MD模拟显示出比ns阶（t（ns））PaCS-MD模拟更高的计算效率，作为循环中的总模拟时间，这表明t（ps）可能适合于有效地产生结构转变。
Parallel cascade selection molecular dynamics (PaCS-MD) has been proposed as a conformational sampling method for enhancing structural transitions from a given reactant to a product by repeating cycles of short-time MD simulations. In the present paper, we assessed how the time scale of a short-time MD simulation affected the computational efficiency by changing the simulation length. In conclusion, ps-order (t(ps)) PaCS-MD simulations showed a higher computational efficiency as a total simulation time over the cycles than ns-order (t(ns)) PaCS-MD simulations, indicating that t(ps) might be suitable for generating structural transitions efficiently.