Gromos-Ckp Dope Simulations (Versions 1 And 2) 271 K

Two GROMOS-CKP DOPE bilayer simulations performed using GROMACS 5.0.6 for 500 ns with different starting velocities. Simulations were performed with a 1.4 nm cut-off with PME for the Coulombic and a 1.4 nm cut-off for the van der Waals interactions with a dispersion correction. These simulations were performed at 271 K with a 128 lipid bilayer. The full trajectories are provided bar the initial 100 ns. The starting structure was taken from an equilibrated DOPE membrane simulated with an older version of the force field which used the PC charges in the head group (see the SI of https://pubs.acs.org/doi/abs/10.1021/jp207013v). The newer PE parameters were constructed using the standard GROMOS lysine parameters.本数据集包含两组基于GROMOS-CKP力场的1,2-二油酰基-sn-甘油-3-磷酸乙醇胺（DOPE）双层膜分子动力学模拟，所有模拟均通过GROMACS 5.0.6软件完成，总时长为500纳秒（ns），且两组模拟采用不同的初始速度参数；模拟体系采用1.4纳米（nm）的相互作用截断半径，其中库仑相互作用通过粒子网格埃瓦尔德求和（Particle Mesh Ewald, PME）方法处理，范德华相互作用同样采用1.4 nm截断半径并附加色散校正；本次模拟均在271开尔文（K）下运行，模拟体系包含由128个脂质分子构成的双层膜结构；本次发布提供完整的模拟轨迹数据，仅排除初始100 ns的时段数据；初始结构取自一套使用旧版力场完成平衡的DOPE膜体系模拟，该旧版力场在膜头部基团中采用了磷脂酰胆碱（Phosphatidylcholine, PC）电荷参数，相关细节可参阅文献https://pubs.acs.org/doi/abs/10.1021/jp207013v的支持信息；新版磷脂酰乙醇胺（Phosphatidylethanolamine, PE）参数通过标准GROMOS赖氨酸参数构建得到。