Constant electric field simulations of the membrane potential illustrated with simple systems.
Constant electric field simulations of the membrane potential illustrated with simple systems.
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DOI：
10.1016/j.bbamem.2011.09.030
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发表时间：
2012-02
影响因子：
3.4
通讯作者：
Roux, Benoit
中科院分区：
文献类型：
--
作者：
Gumbart, James;Khalili-Araghi, Fatemeh;Sotomayor, Marcos;Roux, Benoit
现代计算方法和技术的进步使得基于详细的原子模型对复杂膜蛋白进行广泛的分子动力学模拟成为可能。此类详细模拟的最终目标是产生系统行为尽可能真实的轨迹。在生物膜系统的情况下需要考虑的一个关键方面是跨膜净电势差的存在。对于有意义的计算，重要的是拥有经过充分验证的方法将后者纳入分子动力学模拟中。分子动力学中广泛使用的膜电位处理方法包括施加垂直于膜的外部均匀电场 E。该场作用于整个模拟系统中的所有带电粒子，所产生的施加的膜电势 V 等于施加的电场乘以周期性单元在垂直于膜的方向上的长度。进行了一系列基于简单膜板模型的测试模拟，以阐明应用领域的后果。这些说明性测试表明，恒定场方法是解释生物分子系统分子动力学研究中膜电位的简单而有效的方法。
Advances in modern computational methods and technology make it possible to carry out extensive molecular dynamics simulations of complex membrane proteins based on detailed atomic models. The ultimate goal of such detailed simulations is to produce trajectories in which the behavior of the system is as realistic as possible. A critical aspect that requires consideration in the case of biological membrane systems is the existence of a net electric potential difference across the membrane. For meaningful computations, it is important to have well validated methodologies for incorporating the latter in molecular dynamics simulations. A widely used treatment of the membrane potential in molecular dynamics consists of applying an external uniform electric field E perpendicular to the membrane. The field acts on all charged particles throughout the simulated system, and the resulting applied membrane potential V is equal to the applied electric field times the length of the periodic cell in the direction perpendicular to the membrane. A series of test simulations based on simple membrane-slab models are carried out to clarify the consequences of the applied field. These illustrative tests demonstrate that the constant-field method is a simple and valid approach for accounting for the membrane potential in molecular dynamics studies of biomolecular systems.
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DOI：
10.1021/jz101461d
发表时间：
2011
期刊：
The journal of physical chemistry letters
影响因子：
--
作者：
Jiang W;Hardy DJ;Phillips JC;Mackerell AD Jr;Schulten K;Roux B
通讯作者：
Roux B
影响因子：
3.3
作者：
Delemotte, Lucie;Dehez, Francois;Tarek, Mounir
通讯作者：
Tarek, Mounir
影响因子：
3.8
作者：
Hünenberger, PH;McCammon, JA
通讯作者：
McCammon, JA
影响因子：
3.4
作者：
Gurtovenko, Andrey A.;Vattulainen, Ilpo
通讯作者：
Vattulainen, Ilpo
影响因子：
4.4
作者：
Garate, Jose-Antonio;English, Niall J.;MacElroy, J. M. D.
通讯作者：
MacElroy, J. M. D.