Combining enhanced sampling with experiment-directed simulation of the GYG peptide
Combining enhanced sampling with experiment-directed simulation of the GYG peptide
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DOI：
10.1142/s0219633618400072
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发表时间：
2018-05-01
影响因子：
2.4
通讯作者：
White, Andrew D.
中科院分区：
文献类型：
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作者：
Amirkulova, Dilnoza B.;White, Andrew D.
实验导向模拟(EDS)是一种使分子动力学模拟与实验观测结果相匹配的最小偏差的技术。该方法提高了精度，但没有解决大系统分子动力学模拟的抽样问题。这项工作将EDS与平行回火或平行回火良好回火的集合副本交换方法相结合，以加强采样。这些方法在显性水中的GYG三肽上得到了验证。EDS偏向的集体变量是化学位移，其中设定点由核磁共振实验确定。结果表明，在能谱分析方法中，采用平行回火和平行回火的好回火系综均有可能提高取样质量。这种方法的结合为精确和详尽地模拟生物系统提供了一种新的方法。
Experiment-directed simulation (EDS) is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics simulations of large systems. This work combines EDS with both the parallel-tempering or parallel-tempering well-tempered ensemble replica-exchange methods to enhance sampling. These methods are demonstrated on the GYG tripeptide in explicit water. The collective variables biased by EDS are chemical shifts, where the set-points are determined by NMR experiments. The results show that it is possible to enhance sampling with either parallel-tempering and parallel-tempering well-tempered ensemble in the EDS method. This combination of methods provides a novel approach for both accurately and exhaustively simulating biological systems.