Reconstructing potential energy functions from simulated force-induced unbinding processes
Reconstructing potential energy functions from simulated force-induced unbinding processes
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DOI：
10.1016/s0006-3495(97)78161-x
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发表时间：
1997-09-01
影响因子：
3.4
通讯作者：
Schulten, K
中科院分区：
文献类型：
--
作者：
Balsera, M;Stepaniants, S;Schulten, K
一维随机模型表明，几纳秒的分子动力学模拟可以用来重建大分子结合势的基本特征。这可以通过在施加到分子上的外力的帮助下诱导解结合来实现，并扣除这些力对系统所做的不可逆功。波动耗散定理对这种方法重建结合势的精度设定了基本限制。所得电势的不确定性与模拟过程中对系统做功的不可逆分量成线性比例。这些结果提供了在分子动力学模拟中观察到的能量障碍的先验估计。
One-dimensional stochastic models demonstrate that molecular dynamics simulations of a few nanoseconds can be used to reconstruct the essential features of the binding potential of macromolecules. This can be accomplished by inducing the unbinding with the help of external forces applied to the molecules, and discounting the irreversible work performed on the system by these forces. The fluctuation-dissipation theorem sets a fundamental limit on the precision with which the binding potential can be reconstructed by this method. The uncertainty in the resulting potential is linearly proportional to the irreversible component of work performed on the system during the simulation. These results provide an a priori estimate of the energy barriers observable in molecular dynamics simulations.