Targeted Molecular Dynamics Calculations of Free Energy Profiles Using a Nonequilibrium Friction Correction.
Targeted Molecular Dynamics Calculations of Free Energy Profiles Using a Nonequilibrium Friction Correction.
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DOI：
10.1021/acs.jctc.8b00835
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发表时间：
2018-11
影响因子：
5.5
通讯作者：
Steffen Wolf;G. Stock
中科院分区：
文献类型：
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作者：
Steffen Wolf;G. Stock
由于标准的无偏分子动力学（MD）模拟对于采样罕见事件变得不切实际，“目标MD”采用移动距离约束来强制沿着某些反应坐标x进行罕见跃迁。为了通过Δ G(x) = W(x) - Wdiss(x)从这些非平衡模拟中计算自由能分布，除了（容易获得的）系统上执行的功W(x)外，还需要耗散功Wdiss(x)。通过采用Jarzynski方程的二阶累积展开，结合朗格万理论的分析，耗散功可以通过非平衡摩擦系数ΓNEQ(x)来表示，该系数可以从约束力波动中动态计算。采用NaCl在水中的离子解离作为测试系统，即使在有限数量的模拟和高约束速度下，这种摩擦校正也显示出准确的自由能分布。作为奖励，ΓNEQ(x)的分析可能对摩擦的微观机制产生有价值的见解。
As standard unbiased molecular dynamics (MD) simulations become impractical for sampling rare events, "targeted MD" employs a moving distance constraint to enforce rare transitions along some reaction coordinate x. To calculate free energy profiles from these nonequilibrium simulations via Δ G( x) = W( x) - Wdiss( x), apart from the (readily obtained) work W( x) performed on the system, the dissipated work Wdiss( x) is also required. By employing a second-order cumulant expansion of Jarzynski's equality combined with an analysis within Langevin theory, the dissipated work can be expressed via a nonequilibrium friction coefficient ΓNEQ( x) that may be calculated on-the-fly from constraint force fluctuations. Adopting the ion dissociation of NaCl in water as a test system, this friction correction is shown to result in accurate free energy profiles, even for a modest number of simulations and at high constraint velocities. As a bonus, the analysis of ΓNEQ( x) may yield valuable insight into the microscopic mechanism of friction.