Methodological issues in lipid bilayer simulations
Methodological issues in lipid bilayer simulations
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DOI：
10.1021/jp0348981
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发表时间：
2003-09-04
影响因子：
3.3
通讯作者：
Marrink, SJ
中科院分区：
文献类型：
--
作者：
Anézo, C;de Vries, AH;Marrink, SJ
分子动力学（MD）模拟中的方法学问题，如长程静电相互作用或压力耦合的类型的治疗，观察到的平衡特性有重要的后果。我们报告了一系列长（高达150 ns）的MD模拟二棕榈酰磷脂酰胆碱（DPPC）双层，其中模拟的方法是系统的变化。比较模拟截断方案，埃瓦尔德求和，修改库仑相互作用，无论是由移位函数或反应场模型，描述远程静电指出这些方法中的每一个固有的文物，最重要的是那些直接切断方法。我们进一步表明，双层的性能是不太敏感的压力耦合算法的细节，并增加5 fs的集成时间步长可以安全地用于模拟磷脂酰胆碱脂质双层。
Methodological issues in molecular dynamics (MD) simulations, such as the treatment of long-range electrostatic interactions or the type of pressure coupling, have important consequences for the equilibrium properties observed. We report a series of long (up to 150 ns) MD simulations of dipalmitoylphosphatidylcholine (DPPC) bilayers in which the methodology of simulation is systematically varied. Comparisons of simulations with truncation schemes, Ewald summations, and modified Coulomb interactions, either by shift functions or reaction field models, to describe long-range electrostatics point out the artifacts inherent in each of these methods and above all those of straight cutoff methods. We further show that bilayer properties are less sensitive to the details of the pressure-coupling algorithm and that an increased integration time step of 5 fs can be safely used in simulations of phosphatidylcholine lipid bilayers.