Unbiased simulation of Alanine Dipeptide in gas phase

87 microsecond long unbiased Molecular Dynamics (MD) trajectory of alanine dipeptide in gas phase (traj_comp.xtc). Temperature = 300 K. Force Field: AMBER99SB-ILDN. There are 30+ back and forth transitions between the C_7eq and the C_7ax state. Simulations were performed using GROMACS 2021.4. The .tpr file is provided for reproduction. Details of the simulation parameters are accessible from the md.log file. The phi and psi torsion angles and the internal energy is printed in the COLVAR file at 2 ps interval. Alanine dipeptide is often used as a model system to test new simulation methods. We hope that sharing our long unbiased trajectory will help other research groups to compare the accuracy of the results obtained from new methods. This trajectory was generated as a part of our recent publication below. Please cite the following paper when using this trajectory: 1. Ray, Dhiman, Narjes Ansari, Valerio Rizzi, Michele Invernizzi, and Michele Parrinello. "Rare event kinetics from adaptive bias enhanced sampling." Journal of Chemical Theory and Computation (2022). https://doi.org/10.1021/acs.jctc.2c0080687微秒时长的气相丙氨酸二肽无偏分子动力学（Molecular Dynamics, MD）轨迹文件（traj_comp.xtc）。体系温度为300 K，所用分子力场为AMBER99SB-ILDN。该轨迹中C₇eq与C₇ax构象间存在30余次往复转变。本模拟采用GROMACS 2021.4软件完成，附带.tpr文件以供研究复现。模拟参数的详细信息可从md.log文件中获取。COLVAR文件以2皮秒为间隔记录了φ、ψ二面角与体系内能数据。丙氨酸二肽常被用作测试新型模拟方法的模型体系。我们期望通过共享这条长时长无偏轨迹，助力其他研究团队对比不同新型模拟方法所得结果的准确性。本轨迹生成自我们近期发表的研究工作，使用本轨迹时请引用如下论文：1. Ray, Dhiman, Narjes Ansari, Valerio Rizzi, Michele Invernizzi, and Michele Parrinello. 《基于自适应偏置增强采样的稀有事件动力学》. 《Journal of Chemical Theory and Computation》(2022). https://doi.org/10.1021/acs.jctc.2c00806