Gromos-Ckp Pope Simulations (Versions 1 And 2) 313 K

Two GROMOS-CKP POPE 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 313 K with a 128 lipid bilayer. The full trajectories are provided bar the initial 100 ns. The starting structure was taken from an equilibrated POPE 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POPE（1-棕榈酰基-2-油酰基-sn-甘油-3-磷酸乙醇胺，1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine）双层膜分子动力学模拟，采用GROMACS 5.0.6软件完成，总模拟时长为500 ns，两组模拟采用不同的初始速度。模拟参数设置如下：库仑相互作用采用粒子网格埃瓦尔德（PME，Particle Mesh Ewald）方法，截断半径设为1.4 nm；范德华相互作用同样采用1.4 nm截断半径，并施加色散校正。本模拟体系为包含128个脂质分子的双层膜结构，模拟温度维持在313 K。完整模拟轨迹已提供，初始100 ns的轨迹除外。初始结构取自使用旧版力场完成平衡的POPE膜体系，该旧版力场在头部基团中采用了PC（磷脂酰胆碱，Phosphatidylcholine）电荷，详细信息可参考https://pubs.acs.org/doi/abs/10.1021/jp207013v的补充材料。新版PE力场参数通过标准GROMOS赖氨酸参数构建得到。