title: Trajectory data generated by a virtual-system coupled canonical molecular dynamics simulation with a coarse-grained model of glutamine-octapeptide dimer.
author: Kota Kasahara
description: The trajectory data of the coarse-grained molecular dynamics simulation with the glutamine-octapeptide dimer generated by myPresto/omegagene. The details of simulation is reported in the manuscript "myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling" (doi: 10.2142/biophysico.BSJ-2020013) The file "md.trr" is recorded in GROMACS .trr format, which can be visualized by using some standard molecular viewers such as VMD (https://www.ks.uiuc.edu/Research/vmd/) We recommend visualize the trajectory by using "VDW" or "points" representations for "Drawing Method". The methods depending on connectivity information, e.g., "NewCartoon" and "lines", are not working because of coarse graining. This file included the 10,000 snapshots analyzed in the "Example" section of the manuscript. As described in the manuscript, 10 independent runs of 10^7 steps of simulation were done as production runs. The snapshots were recorded at every 10,000 steps, and 1,000 snapshots were recorded for each run. The "md.trr" file was generated by concatenating these snapshots over 10 runs. The file "q8dimer.pdb" is the initial coordinates of the simulation model. Each atom represents a bead corresponding to one amino acid residue. The cell-dimension of cubic periodic boundary cell is 60 Å.