Dissociation Rate Calculation via Constant-Force Steered Molecular Dynamics Simulation
Dissociation Rate Calculation via Constant-Force Steered Molecular Dynamics Simulation
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DOI：
10.1021/acs.jcim.2c01529
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发表时间：
2023-05-15
影响因子：
5.6
通讯作者：
Kameda，Tomoshi
中科院分区：
文献类型：
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作者：
Iida，Shinji;Kameda，Tomoshi
引导分子动力学 (SMD) 模拟用于通过向分子施加谐波力并以恒定速度拉动它们来研究分子解离事件。我们不使用恒速拉力，而是使用恒力：恒力 SMD (CF-SMD) 模拟。 CF-SMD模拟采用恒定力来降低分子解离的活化势垒，从而增强解离事件。在这里，我们展示了 CF-SMD 模拟估计平衡解离时间的能力。我们对 NaCl 和蛋白质配体系统进行了全原子 CF-SMD 模拟，产生了各种力下的解离时间。我们使用贝尔模型或 Dudko-Hummer-Szabo 模型将这些值外推到没有恒定力的解离速率。我们证明 CF-SMD 模型模拟预测了平衡解离时间。 CF-SMD 模拟是一种强大的工具，可以直接且计算高效的方式估算解离速率。
Steered molecular dynamics (SMD) simulations are used to study molecular dissociation events by applying a harmonic force to the molecules and pulling them at a constant velocity. Instead of constant-velocity pulling, we use a constant force: the constant-force SMD (CF-SMD) simulation. The CF-SMD simulation employs a constant force to reduce the activation barrier of molecular dissociation, thereby enhancing the dissociation event. Here, we present the capability of the CF-SMD simulation to estimate the dissociation time at equilibrium. We performed all-atom CF-SMD simulations for NaCl and protein–ligand systems, producing dissociation time at various forces. We extrapolated these values to the dissociation rate without a constant force using Bell’s model or the Dudko–Hummer–Szabo model. We demonstrate that the CF-SMD simulations with the models predicted the dissociation time in equilibrium. A CF-SMD simulation is a powerful tool for estimating the dissociation rate in a direct and computationally efficient manner.