Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).
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DOI：
10.1016/j.bbagen.2014.09.007
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发表时间：
2015-05
影响因子：
3
通讯作者：
Cheatham, Thomas E., III
中科院分区：
文献类型：
--
作者：
Galindo-Murillo, Rodrigo;Roe, Daniel R.;Cheatham, Thomas E., III
DNA的结构和动力学与其功能密切相关。分子动力学（MD）模拟通过提供有关原子运动的详细信息来增强实验。然而，到目前为止，模拟还没有足够长的时间来收敛的动力学和DNA的结构特性。使用带有parmbsc 0修改的ff 99 SB力场使用AMBER进行的MD模拟，包括独立模拟的集合，与使用专门的Anton MD引擎对B-DNA结构d（GCACGAACGAACGAACGC）进行的长时间尺度MD进行了比较。为了评估收敛性，除了通过主成分投影直方图的Kullback-Leibler发散评估动态的收敛性外，还评估了平均RMSD值在越来越长的时间间隔内的衰减。这些MD模拟-包括迄今为止发表的最长的DNA模拟之一，约44 μ s-令人惊讶地表明，DNA螺旋的结构和动力学，忽略末端碱基对，基本上完全收敛于约1-5 μs的时间尺度。我们现在可以重复收敛的结构和动力学的B-DNA螺旋，省略了末端碱基对，在μs的时间尺度与AMBER和CHARMM C36核酸力场。从不同初始条件开始的独立模拟集合的结果汇总后，与在专门的Anton MD引擎上进行的长时间模拟的结果相匹配。通过访问大规模GPU资源或专门的MD引擎“Anton”，各种分子系统可能可再现地且可靠地会聚采样结构的构象系综。
The structure and dynamics of DNA are critically related to its function. Molecular dynamics (MD) simulations augment experiment by providing detailed information about the atomic motions. However, to date the simulations have not been long enough for convergence of the dynamics and structural properties of DNA. MD simulations performed with AMBER using the ff99SB force field with the parmbsc0 modifications, including ensembles of independent simulations, were compared to long timescale MD performed with the specialized Anton MD engine on the B-DNA structure d(GCACGAACGAACGAACGC). To assess convergence, the decay of the average RMSD values over longer and longer time intervals was evaluated in addition to assessing convergence of the dynamics via the Kullback-Leibler divergence of principal component projection histograms. These MD simulations —including one of the longest simulations of DNA published to date at ~44 μs—surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1–5 μs timescale. We can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the μs time scale with both the AMBER and CHARMM C36 nucleic acid force fields. Results from independent ensembles of simulations starting from different initial conditions, when aggregated, match the results from long timescale simulations on the specialized Anton MD engine. With access to large-scale GPU resources or the specialized MD engine “Anton” it is possibly for a variety of molecular systems to reproducibly and reliably converge the conformational ensemble of sampled structures.
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