CLN025 folding represented via dihedrals or heavy atom distances

41580 frames from a replica-exchange molecular dynamics simulation (400 ns, 340 K replica, dt = 2 fs) of the 10-residue peptide CLN025, which folds into a beta hairpin.<br><br>In "cln025traj_dihedrals.npy" the frames are represented using the 32 dihedral angles of the peptide, given in the following order<br>phi1 phi2 phi3 phi4 phi5 phi6 phi7 phi8 phi9psi1 psi2 psi3 psi4 psi5 psi6 psi7 psi8 psi9chi1_1 chi1_2 chi1_3 chi1_5 chi1_6 chi1_8 chi1_9 chi1_10chi2_1 chi2_2 chi2_3 chi2_5 chi2_9 chi2_10.<br><br>In "cln025traj_distances.npy" the frames are represented using the set of all the 4278 distances between heavy atoms of the molecule.<br><br>The additional files ending with "_decimated_equilibrated" are smaller trajectories generated from the original ones by:- first, taking 1 element every 10 via numpy command array[::10].- then, removing the first 400 elements via array[400:].<br>If you find this dataset useful for your research, please cite the following publication@article{carli2021statistically,title={Statistically unbiased free energy estimates from biased simulations},author={Carli, Matteo and Laio, Alessandro},journal={Molecular Physics},volume={119},number={19-20},pages={e1899323},year={2021},publisher={Taylor \&amp; Francis}}<br><br>本数据集包含41580帧轨迹，源自10残基肽CLN025的复制品交换分子动力学（replica-exchange molecular dynamics）模拟，该模拟总时长400纳秒（ns），对应340开尔文（K）的复制品，时间步长dt=2飞秒（fs），目标肽可折叠为β发夹结构。 在文件"cln025traj_dihedrals.npy"中，每一帧轨迹通过该肽的32个二面角进行表征，其顺序依次为：φ₁、φ₂、φ₃、φ₄、φ₅、φ₆、φ₇、φ₈、φ₉、ψ₁、ψ₂、ψ₃、ψ₄、ψ₅、ψ₆、ψ₇、ψ₈、ψ₉、χ₁_1、χ₁_2、χ₁_3、χ₁_5、χ₁_6、χ₁_8、χ₁_9、χ₁_10、χ₂_1、χ₂_2、χ₂_3、χ₂_5、χ₂_9、χ₂_10。 在文件"cln025traj_distances.npy"中，每一帧轨迹通过该分子所有重原子间的4278组距离进行表征。 后缀为"_decimated_equilibrated"的附加文件为源自原始轨迹的精简平衡轨迹，其生成流程如下： 1. 通过NumPy的array[::10]命令，以每10个元素选取1个的方式进行下采样； 2. 随后通过array[400:]命令移除前400个轨迹帧。 若本数据集对您的研究有所助益，请引用如下文献： @article{carli2021statistically, title={Statistically unbiased free energy estimates from biased simulations}, author={Carli, Matteo and Laio, Alessandro}, journal={Molecular Physics}, volume={119}, number={19-20}, pages={e1899323}, year={2021}, publisher={Taylor & Francis} } 其中期刊《Molecular Physics》标准译名为《分子物理学》，论文标题可译为《有偏模拟中的统计无偏自由能估算》。