Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems
Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems
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DOI：
10.1063/1.478259
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发表时间：
1999-02-22
影响因子：
4.4
通讯作者：
Ballone, P
中科院分区：
文献类型：
--
作者：
Marchi, M;Ballone, P
本研究涉及一种新的分子模拟技术，即绝热偏置分子动力学(MD)，它提供了一种简单且相对廉价的方法来产生由活化势垒分隔的构象空间中的连接点。由于偏置电势在MD运行期间被更新的明智方式，该技术允许在一些额外的工作中计算在轨迹期间经历的自由能变化。绝热偏置方法已被应用于一个不平凡的问题：溶菌酶原子论模型的展开。这里，回转半径(R-g)被用作一个方便的反应坐标。对于R-g在19.7埃和28埃之间的变化，我们观察到溶菌酶天然三级结构的净丢失。同时，二级结构元素，如α-螺旋被保留，尽管一些原来的顺序被减少。计算的展开跃迁自由能分布随R-g单调增加，并与势模型中使用的非键截断密切相关。(C)1999年美国物理研究所。[S0021-9606(99)51708-X]。
This study deals with a novel molecular simulation technique, named adiabatic bias molecular dynamics (MD), which provides a simple and reasonably inexpensive route to generate MD trajectories joining points in conformational space separated by activation barriers. Because of the judicious way the biasing potential is updated during the MD runs, the technique allows with some additional effort the computation of the free energy change experienced during the trajectory. The adiabatic bias method has been applied to a nontrivial problem: The unfolding of an atomistic model of lysozyme. Here, the radius of gyration (R-g) was used as a convenient reaction coordinate. For changes in R-g between 19.7 and 28 Angstrom, we observe a net loss of the native tertiary structure of lysozyme. At the same time, secondary structure elements such as alpha-helices are retained although some of the original order is diminished. The calculated free energy profile for the unfolding transition shows a monotonous increase with R-g and depends crucially on the nonbonded cutoff used in the potential model. (C) 1999 American Institute of Physics. [S0021-9606(99)51708-X].