On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations.
On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations.
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DOI：
10.1021/ct100605v
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发表时间：
2011-04-12
影响因子：
5.5
通讯作者：
Markwick, Phineus R. L.
中科院分区：
文献类型：
--
作者：
Bucher, Denis;Pierce, Levi C. T.;McCammon, J. Andrew;Markwick, Phineus R. L.
我们已经实施了加速分子动力学方法（Hamelberg，D.; Mongan，J.; McCammon，J. A. 2004，120（24），11919）在从头算MD（AIMD）的框架中。使用三个简单的例子，我们证明了加速AIMD（A-AIMD）可用于加速AIMD模拟中的溶剂弛豫，并有助于检测反应坐标：（i）我们表明，对于气相中的一个环己烷分子，该方法可用于将椅子-椅子相互转化的速率加快10.1 × 105倍，同时允许重建低能态的正确正则分布;（ii）然后，我们表明，对于64个H2O分子的水箱，A-AIMD也可以用于凝聚相，以加速水构象的采样，而不影响溶剂的结构特性;以及（iii）然后使用该方法计算Na−Cl在水中解离的平均力势（PMF），与传统AIMD模拟相比，收敛速度加快了103 −4倍。这些结果表明，A-AIMD是一个有用的除了现有的方法，增强构象和相空间采样的解决方案。虽然该方法不使集体变量的使用是多余的，但它也不要求用户定义一组集体变量，这些变量可以捕获势能面上的所有低能最小值。这个性质在处理需要量子力学处理的高度复杂的多维系统时可能非常有用。
We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ∼1 × 105, while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H2O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na−Cl in water, accelerating the convergence by a factor of ∼3−4 compared to conventional AIMD simulations. These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment.
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影响因子：
4.4
作者：
Hura, G;Sorenson, JM;Head-Gordon, T
通讯作者：
Head-Gordon, T
影响因子：
1.7
作者：
Martyna, GJ;Tuckerman, ME;Klein, ML
通讯作者：
Klein, ML
DOI：
10.1073/pnas.202427399
发表时间：
2002-10-01
影响因子：
11.1
作者：
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通讯作者：
Parrinello, M
影响因子：
3.6
作者：
Gill, G;Pawar, DM;Noe, EA
通讯作者：
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影响因子：
15
作者：
Markwick, Phineus R. L.;Bouvignies, Guillaume;Salmon, Loic;McCammon, J. Andrew;Nilges, Michael;Blackledge, Martin
通讯作者：
Blackledge, Martin