Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers.
Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers.
复制标题
用于模拟脂质双层和单层的扩展各向同性周期和与粒子网格 Ewald 方法的比较。
DOI：
10.1021/jp900843x
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发表时间：
2009
期刊：
影响因子：
--
通讯作者：
Pastor,RichardW
中科院分区：
文献类型：
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作者：
Venable,RichardM;Chen,LindaE;Pastor,RichardW
3D-IPS/DFFT是三维各向同性周期和（3D-IPS）的扩展，用于评估非均质系统中的静电和Lennard-Jones相互作用;它利用离散快速傅里叶变换（DFFT）来有效计算具有大局部区域半径的IPS势。该方法被证明是高度准确的简单的散装流体，液体/液体和液体/蒸汽界面，脂质双层和单层。rC（直接评估对的截止距离）和RC（局部区域半径）的值分别等于10 μ m和周期单元最长边的两倍，提供了出色的效率和精度。用CHARMM（哈佛分子力学化学）C27 r脂质参数集和3D-IPS/DFFT模拟的二肉豆蔻酰磷脂酰胆碱（DMPC）单层产生的表面张力比使用粒子网格Ewald（PME）和实验模拟的表面张力高约8 dyn/cm。相比之下，DMPC双层的表面张力为16 dyn/cm/瓣叶，具有3D-IPS/DFFT（rC= 10和12 μ m）和PME（rC= 12 μ m）。这表明PME（rC= 12 Ω）可以用于模拟双层，但不能用于单层，并且由C27 r引起的大的双层表面张力是不正确的。
3D-IPS/DFFT is an extension of the three-dimensional isotropic periodic sum (3D-IPS) for evaluation of electrostatic and Lennard-Jones interactions in heterogeneous systems; it utilizes a discrete fast Fourier transform (DFFT) for efficient calculation of the IPS potential with a large local region radius. The method is demonstrated to be highly accurate for simple bulk fluids, liquid/liquid and liquid/vapor interfaces, and lipid bilayers and monolayers. Values forrC(the cutoff distance for direct evaluation of pairs) andRC(the local region radius) equal to 10 Å and twice the longest edge of the periodic cell, respectively, provide excellent efficiency and accuracy. Dimyristoylphosphatidylcholine (DMPC) monolayers simulated with the CHARMM (Chemistry at HARvard Molecular Mechanics) C27r lipid parameter set and 3D-IPS/DFFT yield surface tensions approximately 8 dyn/cm higher than those simulated using particle mesh Ewald (PME), and with experiment. In contrast, surface tensions for DMPC bilayers are 16 dyn/cm/leaflet with both 3D-IPS/DFFT (rC= 10 and 12 Å) and PME (rC= 12 Å). This indicates that PME (rC= 12 Å) may be used for simulations of bilayers, but not monolayers, and that the large bilayer surface tension arising from C27r is incorrect.