Berger Dope Simulations (Versions 1 And 2) 271 K - De Vries Repulsive H

Two Berger-based DOPE bilayer simulations performed using GROMACS 4.0.7 for 200 ns with different starting velocities. Simulations were performed with a 1.0 nm cut-off with PME for the Coulombic and a 1.0 nm cut-off for the van der Waals interactions with a dispersion correction. These simulations were performed at 303 K with a 128 lipid bilayer. The full trajectories are provided bar the initial 100 ns. The starting structure was converted from an equilibrated DOPC membrane simulated with the GROMOS-CKP force field. The DOPE parameters were constructed following the approach used by de Vries et al (https://pubs.acs.org/doi/abs/10.1021/jp0366926), and so include a small repulsive potential on the explicit hydrogen atoms.本数据集包含两项基于Berger力场的DOPE（1,2-二油酰-sn-甘油-3-磷酸乙醇胺）双层膜分子动力学模拟，采用GROMACS 4.0.7软件完成，总模拟时长为200纳秒，两组模拟的初始速度参数存在差异。模拟过程中，库仑相互作用采用粒子网格埃瓦尔德（PME，Particle Mesh Ewald）方法处理，截断半径设为1.0纳米；范德华相互作用同样采用1.0纳米截断半径，并添加了色散校正项。所有模拟均在303开尔文的温度下进行，体系包含128个脂质分子构成的双层膜结构。完整的模拟轨迹已提供，仅剔除了初始100纳秒的时段数据。模拟初始结构源自使用GROMOS-CKP力场模拟得到的平衡态DOPC（1,2-二油酰基-sn-甘油-3-磷酸胆碱）膜结构。DOPE力场参数参照de Vries等学者的研究方法构建（详见文献链接：https://pubs.acs.org/doi/abs/10.1021/jp0366926），该参数包含针对显性氢原子的微小排斥势。