Simulation Trajectories: "Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor"

* Simulations described in the following paper:Miao Y & McCammon JA (2016) Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor. Proc Natl Acad Sci U S A, 113(43):12162–12167. PMCID: PMC5087018.
* Simulation lengths: system 4mqs-apo-pro-mem-wb-0.15MID 1 2 3duration(ns) 410 460 430
system 3uon-apo-c36-pro-mem-wb-0.15MID 1 2 3duration(ns) 400 400 400
system 3uon-c36-pro-mem-wb-0.15MID 1 2 3duration(ns) 405 405 400
system 4mqs-nb-arc-pro-mem-wb-0.15MID 1 2 3duration(ns) 402 405 400
system 4mqs-nb-ixo-pro-mem-wb-0.15MID 1 3 2duration(ns) 500 400 500
system 4mqs-arc-pro-mem-wb-0.15MID 1 2 3 4 5 6 7 8 9 10duration(ns) 2030 1520 1190 650 650 650 620 600 600 540
system 4mqs-ixo-pro-mem-wb-0.15MID 1 2 3 4 5 6 7 8 9 10duration(ns) 1050 1000 940 500 500 500 500 480 450 410
* List of simulation trajectores:3uon-c36-pro-mem-wb-0.15M-sim-1.nc3uon-c36-pro-mem-wb-0.15M-sim-2.nc3uon-c36-pro-mem-wb-0.15M-sim-3.nc4mqs-arc-pro-mem-wb-0.15M-sim-1.nc4mqs-arc-pro-mem-wb-0.15M-sim-2.nc4mqs-arc-pro-mem-wb-0.15M-sim-3.nc4mqs-arc-pro-mem-wb-0.15M-sim-4.nc4mqs-arc-pro-mem-wb-0.15M-sim-5.nc4mqs-arc-pro-mem-wb-0.15M-sim-6.nc4mqs-arc-pro-mem-wb-0.15M-sim-7.nc4mqs-arc-pro-mem-wb-0.15M-sim-8.nc4mqs-arc-pro-mem-wb-0.15M-sim-9.nc4mqs-arc-pro-mem-wb-0.15M-sim-10.nc4mqs-ixo-pro-mem-wb-0.15M-sim-1.nc4mqs-ixo-pro-mem-wb-0.15M-sim-2.nc4mqs-ixo-pro-mem-wb-0.15M-sim-3.nc4mqs-ixo-pro-mem-wb-0.15M-sim-4.nc4mqs-ixo-pro-mem-wb-0.15M-sim-5.nc4mqs-ixo-pro-mem-wb-0.15M-sim-6.nc4mqs-ixo-pro-mem-wb-0.15M-sim-7.nc4mqs-ixo-pro-mem-wb-0.15M-sim-8.nc4mqs-ixo-pro-mem-wb-0.15M-sim-9.nc4mqs-ixo-pro-mem-wb-0.15M-sim-10.nc4mqs-nb-arc-pro-mem-wb-0.15M-sim-1.nc4mqs-nb-arc-pro-mem-wb-0.15M-sim-2.nc4mqs-nb-arc-pro-mem-wb-0.15M-sim-3.nc4mqs-nb-ixo-pro-mem-wb-0.15M-sim-1.nc4mqs-nb-ixo-pro-mem-wb-0.15M-sim-2.nc4mqs-nb-ixo-pro-mem-wb-0.15M-sim-3.nc
stride: 100 ps / frame
* PSF/PDB files for loading the trajectories:3uon-apo-c36-pro-mem-wb-0.15M-pro.pdb3uon-apo-c36-pro-mem-wb-0.15M-pro.psf3uon-c36-pro-mem-wb-0.15M-pro.pdb3uon-c36-pro-mem-wb-0.15M-pro.psf4mqs-apo-pro-mem-wb-0.15M-pro.pdb4mqs-apo-pro-mem-wb-0.15M-pro.psf4mqs-arc-pro-mem-wb-0.15M-pro.pdb4mqs-arc-pro-mem-wb-0.15M-pro.psf4mqs-ixo-pro-mem-wb-0.15M-pro.pdb4mqs-ixo-pro-mem-wb-0.15M-pro.psf4mqs-nb-arc-pro-mem-wb-0.15M-pro.pdb4mqs-nb-arc-pro-mem-wb-0.15M-pro.psf4mqs-nb-ixo-pro-mem-wb-0.15M-pro.pdb4mqs-nb-ixo-pro-mem-wb-0.15M-pro.psf

- 本数据集基于下述论文中的分子模拟研究：Miao Y与McCammon JA（2016）《毒蕈碱型G蛋白偶联受体的分级激活与自由能景观》，发表于《美国国家科学院院刊》，2016年，113卷（43期）：12162–12167，PMCID编号：PMC5087018。
- 模拟时长统计如下：
系统：4mqs-apo-pro-mem-wb-0.15MID，三次模拟时长（单位：纳秒，ns）分别为410、460、430
系统：3uon-apo-c36-pro-mem-wb-0.15MID，三次模拟时长分别为400、400、400
系统：3uon-c36-pro-mem-wb-0.15MID，三次模拟时长分别为405、405、400
系统：4mqs-nb-arc-pro-mem-wb-0.15MID，三次模拟时长分别为402、405、400
系统：4mqs-nb-ixo-pro-mem-wb-0.15MID，三次模拟时长分别为500、400、500
系统：4mqs-arc-pro-mem-wb-0.15MID，十次模拟时长分别为2030、1520、1190、650、650、650、620、600、600、540（单位：纳秒）
系统：4mqs-ixo-pro-mem-wb-0.15MID，十次模拟时长分别为1050、1000、940、500、500、500、500、480、450、410（单位：纳秒）
- 模拟轨迹文件列表如下：
3uon-c36-pro-mem-wb-0.15M-sim-1.nc
3uon-c36-pro-mem-wb-0.15M-sim-2.nc
3uon-c36-pro-mem-wb-0.15M-sim-3.nc
4mqs-arc-pro-mem-wb-0.15M-sim-1.nc
4mqs-arc-pro-mem-wb-0.15M-sim-2.nc
4mqs-arc-pro-mem-wb-0.15M-sim-3.nc
4mqs-arc-pro-mem-wb-0.15M-sim-4.nc
4mqs-arc-pro-mem-wb-0.15M-sim-5.nc
4mqs-arc-pro-mem-wb-0.15M-sim-6.nc
4mqs-arc-pro-mem-wb-0.15M-sim-7.nc
4mqs-arc-pro-mem-wb-0.15M-sim-8.nc
4mqs-arc-pro-mem-wb-0.15M-sim-9.nc
4mqs-arc-pro-mem-wb-0.15M-sim-10.nc
4mqs-ixo-pro-mem-wb-0.15M-sim-1.nc
4mqs-ixo-pro-mem-wb-0.15M-sim-2.nc
4mqs-ixo-pro-mem-wb-0.15M-sim-3.nc
4mqs-ixo-pro-mem-wb-0.15M-sim-4.nc
4mqs-ixo-pro-mem-wb-0.15M-sim-5.nc
4mqs-ixo-pro-mem-wb-0.15M-sim-6.nc
4mqs-ixo-pro-mem-wb-0.15M-sim-7.nc
4mqs-ixo-pro-mem-wb-0.15M-sim-8.nc
4mqs-ixo-pro-mem-wb-0.15M-sim-9.nc
4mqs-ixo-pro-mem-wb-0.15M-sim-10.nc
4mqs-nb-arc-pro-mem-wb-0.15M-sim-1.nc
4mqs-nb-arc-pro-mem-wb-0.15M-sim-2.nc
4mqs-nb-arc-pro-mem-wb-0.15M-sim-3.nc
4mqs-nb-ixo-pro-mem-wb-0.15M-sim-1.nc
4mqs-nb-ixo-pro-mem-wb-0.15M-sim-2.nc
4mqs-nb-ixo-pro-mem-wb-0.15M-sim-3.nc
采样步长：每帧对应100皮秒（ps）
- 用于加载轨迹的PSF/PDB结构文件（Protein Structure File/Protein Data Bank File）列表如下：
3uon-apo-c36-pro-mem-wb-0.15M-pro.pdb
3uon-apo-c36-pro-mem-wb-0.15M-pro.psf
3uon-c36-pro-mem-wb-0.15M-pro.pdb
3uon-c36-pro-mem-wb-0.15M-pro.psf
4mqs-apo-pro-mem-wb-0.15M-pro.pdb
4mqs-apo-pro-mem-wb-0.15M-pro.psf
4mqs-arc-pro-mem-wb-0.15M-pro.pdb
4mqs-arc-pro-mem-wb-0.15M-pro.psf
4mqs-ixo-pro-mem-wb-0.15M-pro.pdb
4mqs-ixo-pro-mem-wb-0.15M-pro.psf
4mqs-nb-arc-pro-mem-wb-0.15M-pro.pdb
4mqs-nb-arc-pro-mem-wb-0.15M-pro.psf
4mqs-nb-ixo-pro-mem-wb-0.15M-pro.pdb
4mqs-nb-ixo-pro-mem-wb-0.15M-pro.psf