Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations
Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations
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DOI：
10.1063/1.1574777
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发表时间：
2003-06-15
影响因子：
4.4
通讯作者：
Kevrekidis, IG
中科院分区：
文献类型：
--
作者：
Hummer, G;Kevrekidis, IG
我们提出了一种“粗分子动力学”的方法，并将其应用于研究多肽片段在水中溶解的动力学和热力学。使用适当初始化的短脉冲模拟来推断由适当的粗变量集参数化的肽运动的确定性和随机性分量。因此，来自传统数值分析的技术(牛顿-拉夫森、粗略投影积分)被启用；这些技术有助于分析自由能景观的重要特征(粗略过渡态、本征值和特征向量、过渡率等)。粗变量在时间上的反向积分可以帮助逃脱自由能极小值，并跟踪低维自由能表面。为了说明粗分子动力学方法，我们结合多个短的(0.5ps)复制模拟来绘制“丙氨酸二肽”在水中的自由能表面，并确定与α-螺旋和扩展极小值相对应的两个稳定构型盆地之间类似于1/(1000ps)的相互转化速率。(C)2003年美国物理研究所。
We present a "coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic and stochastic components of the peptide motion parametrized by an appropriate set of coarse variables. Techniques from traditional numerical analysis (Newton-Raphson, coarse projective integration) are thus enabled; these techniques help analyze important features of the free-energy landscape (coarse transition states, eigenvalues and eigenvectors, transition rates, etc.). Reverse integration of coarse variables backward in time can assist escape from free energy minima and trace low-dimensional free energy surfaces. To illustrate the coarse molecular dynamics approach, we combine multiple short (0.5 ps) replica simulations to map the free energy surface of the "alanine dipeptide'' in water, and to determine the similar to1/(1000 ps) rate of interconversion between the two stable configurational basins corresponding to the alpha-helical and extended minima. (C) 2003 American Institute of Physics.