Met-enkephalin MD Trajectories

Ten ~50 ns molecular dynamics (MD) simulation trajectories of the 5 residue Met-enkaphalin peptide. The aggregate sampling is 499.58 ns. Simulations were performed starting from the 1st model in the 1PLX PDB file, solvated with 832 TIP3P water molecules using OpenMM 6.0. The coordinates (protein only -- the water was stripped) are saved every 5 picoseconds. Each of the ten trajectories is roughly 50 ns long and contains about 10,000 snapshots. Forcefield: amber99sb-ildn; water: tip3p; nonbonded method: PME; cutoffs: 1nm; bonds to hydrogen were constrained; integrator: langevin dynamics; temperature: 300K; friction coefficient: 1.0/ps; pressure control: Monte Carlo barostat (interval of 25 steps); timestep 2 fs.本数据集包含10条针对5残基甲硫氨酸脑啡肽肽段的、时长约50纳秒的分子动力学（molecular dynamics, MD）模拟轨迹，总采样时长共计499.58纳秒。模拟以1PLX号蛋白质数据库（PDB）文件中的首个模型作为初始结构，通过OpenMM 6.0软件完成体系搭建，使用832个TIP3P水分子进行溶剂化处理。每5皮秒保存一次体系坐标（仅保留蛋白质原子坐标，已剔除水分子）。单条轨迹时长约50纳秒，10条轨迹各包含约10000个构象快照。本次模拟的参数设置如下：力场选用amber99sb-ildn，水分子模型为TIP3P；非键相互作用计算采用粒子网格埃瓦尔德（Particle Mesh Ewald, PME）方法，截断距离设置为1纳米；与氢原子相连的化学键均被约束；积分器选用朗之万动力学，模拟温度维持300开尔文，摩擦系数为1.0每皮秒；压力调控采用蒙特卡洛恒压器，调控步长间隔为25步；时间步长设置为2飞秒。