title: Unbiased simulation of Alanine Dipeptide in gas phase
author: Dhiman Ray
description: 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.2c00806 