Izvekov Sergei, Voth Gregory A
Department of Chemistry and Center for Biophysical Modeling and Simulation, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112-0850.
J Chem Theory Comput. 2006 May;2(3):637-48. doi: 10.1021/ct050300c.
Coarse-grained (CG) models for mixed dimyristoylphosphatidylcholine (DMPC)/cholesterol lipid bilayers are constructed using the recently developed multiscale coarse-graining (MS-CG) method. The MS-CG method permits a systematic fit of the bonded and nonbonded interactions and system pressure to trajectory and force data derived from an underlying reference all-atom molecular dynamics (MD) simulation. The CG sites for lipid and cholesterol molecules are associated with the centers-of-mass of atomic groups because of the simplicity in the evaluation of the forces acting on them from the atomistic MD data. Corresponding models with four-site and seven-site representations of the cholesterol molecule were also developed. The latter CG models differed by the bonding scheme of CG sites to represent intramolecular interactions. A one-site MS-CG model based on the TIP3P potential was used for water, with the interaction site placed at the molecular geometrical center, and the analytical fit of the model is presented. The MS-CG models were then used to conduct simulations in the constant NPT ensemble which reproduce accurately the structural properties as seen in the full all-atom MD simulation.
使用最近开发的多尺度粗粒化（MS-CG）方法构建了混合二肉豆蔻酰磷脂酰胆碱（DMPC）/胆固醇脂质双层的粗粒化（CG）模型。MS-CG方法允许将键合和非键合相互作用以及系统压力系统地拟合到从基础参考全原子分子动力学（MD）模拟得出的轨迹和力数据。由于从原子MD数据评估作用在脂质和胆固醇分子上的力很简单，因此脂质和胆固醇分子的CG位点与原子团的质心相关联。还开发了具有胆固醇分子的四点和七点表示的相应模型。后一种CG模型在CG位点的键合方案上有所不同，以表示分子内相互作用。基于TIP3P势的单点MS-CG模型用于水，相互作用位点位于分子几何中心，并给出了该模型的解析拟合。然后使用MS-CG模型在恒定NPT系综中进行模拟，该模拟准确地再现了全原子MD模拟中所见的结构特性。
