Molecular dynamics simulation data for the publication "Auxiliary subunits reshape structural asymmetry and functional plasticity in heterotetrameric GluA1/A2 AMPA receptor core"

This dataset contains molecular dynamics simulation trajectories and the initial coordinates for the production runs of all simulated structures. Description of the Data and File Structure The data are deposited as a .zip file and organized into 4 folders, each containing MD simulation data for GluA1/A2Glu+RR2b, GluA1/A2-y8Open, GluA1/A2-CNIH2-y8Open, and GluA1/A2ZK systems. All prodcution trajectory (.nc) files were saved at 400 picosecond intervals starting from the first frame. Please see the table below for the systems and their corresponding topology and trajectory files. System # of Frames Production Length Topology File Trajectory File GluA1/A2Glu+RR2b 1236 494 ns AMPAR_A1A2_HMR.prmtop AMPAR_A1A2_traj_prod_skip20.nc GluA1/A2-y8Open 1242 498 ns AMPAR_A1A2_Y8_HMR.prmtop AMPAR_A1A2_Y8_traj_prod_skip20.nc GluA1/A2-CNIH2-y8Open 1120 448 ns AMPAR_A1A2_Y8_CNIH2_HMR.prmtop AMPAR_A1A2_Y8_CNIH2_traj_prod_skip20.nc GluA1/A2ZK 991 396 ns AMPAR_A1A2_ZK_HMR.prmtop AMPAR_A1A2_ZK_traj_prod_skip20.nc The initial structures for the production trajectories, along with their corresponding topology files, are located within each system folder. The topology files use the .prmtop format, and the coordinate files use the .rst7 format. MD production trajectories in binary NetCDF (.nc) format and the coordinate files can be visualized using VMD after loading the corresponding topology file. Analysis of the trajectories can be performed using the CPPTRAJ module of AmberTools and VMD.