MD simulation trajectory for EGFR TM region with L658Q mutation in ordered membrane

Coarse-grained molecular dynamics trajectory of the EGFR L658Q transmembrane-juxtamembrane (TM-JM) peptide dimer (residues 654-695, PDB 2M20) in an ordered membrane (DIPC/DPSM/CHOL, equimolar upper leaflet). Simulated with GROMACS 2023.3 using the MARTINI 2.2 force field with polarizable water. Four peptide copies in a 40 x 40 nm periodic box, 0.15 M NaCl, 298 K. Trajectory frames saved every 1 ns. Associated with: Sato & Tamagaki-Asahina, "A conformational directivity switch imposed by the membrane in receptor tyrosine kinase dimers" and Sato, "CASCADE and MERIT — frameworks for extracting the directivity and causal architecture of structural covariation in molecular dynamics trajectories.本数据集为表皮生长因子受体（EGFR）L658Q突变体跨膜-近膜区（transmembrane-juxtamembrane, TM-JM）肽二聚体（残基编号654-695，对应蛋白质数据库（Protein Data Bank, PDB）条目2M20）在有序复合膜（DIPC/DPSM/CHOL，上层小叶采用等摩尔比配比）中的粗粒度分子动力学（coarse-grained molecular dynamics）轨迹。模拟使用GROMACS 2023.3软件完成，力场采用MARTINI 2.2力场并搭配极化水（polarizable water）模型。模拟体系置于40×40 nm的周期性盒子中，内含4份该肽段，盐浓度为0.15 M NaCl，体系温度维持在298 K。轨迹每1纳秒保存一帧。本数据集关联两篇研究：Sato与Tamagaki-Asahina发表的《膜赋予受体酪氨酸激酶二聚体的构象方向性开关》，以及Sato发表的《CASCADE与MERIT——提取分子动力学轨迹中结构共变的方向性与因果架构的框架》。