Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel.
Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel.
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混合原子和粗粒度分子动力学：膜结合离子通道的模拟。
DOI：
10.1021/jp062700h
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发表时间：
2006
期刊：
影响因子：
--
通讯作者：
Voth,GregoryA
中科院分区：
文献类型：
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作者：
Shi,Qiang;Izvekov,Sergei;Voth,GregoryA
最近开发的多尺度粗粒化（MS-CG）方法（Izvekov，S.;沃斯湾A.J.Phys.Chem.B2005，109，2469; J.Chem.Phys.2005，123，134105）用于构建嵌入二肉豆蔻酰磷脂酰胆碱（DMPC）脂质双层和水环境中的短杆菌肽A（gA）离子通道的混合全原子和粗粒（AA-CG）模型。在这个模型中，gA肽被描述在完整的原子细节，而脂质和水分子被描述使用粗粒度的表示。用MS-CG方法计算了AA-CG混合模型中原子-CG和CG-CG相互作用。使用所得AA-CG模型进行分子动力学（MD）模拟。AA-CG模型的模拟结果与整个系统的全原子MD模拟结果相比非常有利。由于MS-CG方法采用了一种通用和系统的方法来获得有效的相互作用，从底层的全原子模型，本方法严格开发混合AA-CG模型有可能被扩展到许多其他系统。
The recently developed multiscale coarse-graining (MS-CG) method (Izvekov, S.; Voth, G. A.J. Phys. Chem. B2005,109, 2469;J. Chem.Phys.2005,123, 134105) is used to build a mixed all-atom and coarse-grained (AA-CG) model of the gramicidin A (gA) ion channel embedded in a dimyristoylphosphatidylcholine (DMPC) lipid bilayer and water environment. In this model, the gA peptide was described in full atomistic detail, while the lipid and water molecules were described using coarse-grained representations. The atom-CG and CG-CG interactions in the mixed AA-CG model were determined using the MS-CG method. Molecular dynamics (MD) simulations were performed using the resulting AA-CG model. The results from simulations of the AA-CG model compare very favorably to those from all-atom MD simulations of the entire system. Since the MS-CG method employs a general and systematic approach to obtain effective interactions from the underlying all-atom models, the present approach to rigorously develop mixed AA-CG models has the potential to be extended to many other systems.