The folders contain simulation data associated with the H3/CENP-A octasomes and the steered MD of 6o1d using the amber999bsc1 forcefield.

In total, there are nine different systems, consisting of MD simulation data for the H3/CENP-A octasomes and a steered MD for the 6o1d system. Four of these systems belong to the H3/CENP-A octasomes. Each of them represents a specific structure:

- sys1: cryo-EM structure (without histone tails and DNA ends)
        total simulation time: 500 ns

- sys2: cryo-EM structure with added DNA ends 
        total simulation time: 500 ns

- sys3: cryo-EM structure with added histone tails
        total simulation time: 500 ns

- sys4: complete nucleosome core particle with added DNA and histone tails
        total raw simulation time: 500 ns (CENP-A) and ~ 1110 ns (H3)
        reduced frames of protein-DNA complex: 900 ns without the first 100 ns (CENP-A and H3)

- sys_steeredMD: steered MD of 6o1d with target set to the tetramer 3NQJ (PDB ID)
                 total simulation time: ~ 247 ns

The directories sys_1 to sys_4 are divided into the H3 and CENP-A cases.
Each case folder contains files in GROMACS format, such as the topology, initial coordinates, index, and trajectories. For the steered MD simulation of the 6o1d system, the target was the 3NQJ tetramer, and the folder contains additional COLVAR files obtained from PLUMED with the collective variable set to the RMSD.

The reducedframes folder contains the reduced trajectory with a time step of 100 ps, which contains only the protein-DNA complex from which the roto-translational motion had been removed by fitting the structure to the C𝛼 atoms part of the histone fold domain of the first frame of this trajectory. For the octasomes, the first 100 ns of the production run are not included in the reduced trajectory. A corresponding pdb file of the first frame is also provided.

The file mdp_octasomes.mdp contains the mdp input for the production run of all the octasomes. The parameter files for the steered MD are in the sys_steeredMD folder. For the first 100000 steps, plumed.dat was used and after that always plumed_from_part0002.dat.