Pure POPC Membrane with 650mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM

500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 76 CaCl2, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. The initial structures have been obtained from CHARMM-GUI. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>本数据集为采用Charmm-Drude极化力场开展的纯1-棕榈酰-2-油酰基-sn-甘油-3-磷酸胆碱（POPC）膜500纳秒（nanosecond, ns）分子动力学（Molecular Dynamics, MD）模拟。模拟体系包含128个POPC脂质分子、76个氯化钙（CaCl₂）单元与6400个SWM4水分子模型。本次模拟通过OpenMM 7.4.1平台完成。在启动Drude模拟前，体系已使用Charmm36力场完成200纳秒的平衡模拟，该平衡模拟的最终帧被用于构建Drude极化力场模型。本数据集剔除了Drude模拟的前100纳秒数据。wrapped.dcd轨迹的帧保存频率为100皮秒（picosecond, ps）。初始结构源自CHARMM-GUI平台。经核查（详见链接：https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243），wrapped_full.dcd轨迹文件存在时间戳错误：连续模拟帧之间的时间步长未正确嵌入轨迹信息中。为此，我们在本次更新中上传了具备正确时间戳的"wrapped_full_fixed_dt.xtc"文件，该轨迹的帧保存频率为10皮秒（ps）。本次更新不会对未从轨迹文件中显式读取时间戳信息的既往计算结果产生影响。本次模拟包含5个子轨迹，每个子轨迹均以上一个子轨迹的最终帧作为起始，并运行100纳秒。这些原本为dcd格式的轨迹经MDAnalysis工具拼接并转换为xtc格式存储。