Accelerating Membrane Simulations with Hydrogen Mass Repartitioning
Accelerating Membrane Simulations with Hydrogen Mass Repartitioning
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DOI：
10.1021/acs.jctc.9b00160
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发表时间：
2019-08-01
影响因子：
5.5
通讯作者：
Gumbart, James C.
中科院分区：
文献类型：
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作者：
Balusek, Curtis;Hwang, Hyea;Gumbart, James C.
原子分子动力学（MD）模拟的时间步长由系统中最快的运动决定，通常限制为2 fs。一种越来越流行的方法是将氢原子的质量增加到接近3 amu，并将母体原子的质量减少等量。这种方法被称为氢质量再分配（HMR），允许时间步长高达4 fs，具有合理的模拟稳定性。虽然HMR已被应用于许多已发表的研究，但它尚未被广泛测试含膜系统。在这里，我们比较了各种膜和膜蛋白质系统的模拟结果运行使用2 fs的时间步长和4 fs的时间步长与HMR对于纯膜系统，我们发现几乎没有差异的结构特性，如面积每脂质，电子密度分布和顺序参数，虽然有不同的动力学性质，如扩散常数。通过一个孔蛋白在一个应用领域，分区的小肽，氢键动力学，和膜混合的电导表现出很小的依赖HMR和时间步长。我们还测试了9埃截止相比，标准的CHARMM截止的12埃，发现显着的偏差，在许多性能测试。我们的结论是，HMR是一个有效的方法，膜系统，但9埃截止不是。
The time step of atomistic molecular dynamics (MD) simulations is determined by the fastest motions in the system and is typically limited to 2 fs. An increasingly popular approach is to increase the mass of the hydrogen atoms to similar to 3 amu and decrease the mass of the parent atom by an equivalent amount. This approach, known as hydrogen-mass repartitioning (HMR), permits time steps up to 4 fs with reasonable simulation stability. While HMR has been applied in many published studies to date, it has not been extensively tested for membrane-containing systems. Here, we compare the results of simulations of a variety of membranes and membrane-protein systems run using a 2 fs time step and a 4 fs time step with HMR For pure membrane systems, we find almost no difference in structural properties, such as area-per-lipid, electron density profiles, and order parameters, although there are differences in kinetic properties such as the diffusion constant. Conductance through a porin in an applied field, partitioning of a small peptide, hydrogen-bond dynamics, and membrane mixing show very little dependence on HMR and the time step. We also tested a 9 angstrom cutoff as compared to the standard CHARMM cutoff of 12 angstrom, finding significant deviations in many properties tested. We conclude that HMR is a valid approach for membrane systems, but a 9 angstrom cutoff is not.