Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
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DOI：
10.1063/1.1755656
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发表时间：
2004-06-22
影响因子：
4.4
通讯作者：
McCammon, JA
中科院分区：
文献类型：
--
作者：
Hamelberg, D;Mongan, J;McCammon, JA
由于纳秒时间尺度的限制，生物分子的许多有趣的动力学性质不能直接使用分子动力学模拟。这些系统被困在势能极小值与高的自由能势垒为大量的计算步骤。许多分子系统的动态演化是通过一系列罕见的事件发生的，因为系统从一个势能盆地移动到另一个势能盆地。因此，我们提出了一个强大的偏置势函数，可用于一个有效的加速分子动力学方法来模拟过渡的高能量障碍，而无需任何预先知道的位置的势能威尔斯或鞍点。在该方法中，通过向真实势添加偏置势来改变势能景观，使得从势威尔斯的逃逸率增强，这加速并扩展了分子动力学模拟中的时间尺度。我们对偏置势的定义与修改后表面上势能景观的基本形状相呼应，从而可以很好地定义势能最小值，从而在模拟过程中正确采样。我们已经表明，我们的方法，它可以扩展到生物分子，样品的构象空间比正常的分子动力学模拟更有效，并收敛到正确的正则分布。(C)2004年，美国物理学会。
Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution. (C) 2004 American Institute of Physics.