Modulation of α-Synuclein Aggregation Amid Diverse Environmental Perturbation

The zip file contains the following raw trajectory data between 1.5 to 2.0 us obtained from molecular dynamics (MD) simulations of 50 alpha-synuclein (aS) chains in a cubic box with a concentration of 750 uM. Three different environments have been simulated in this study: aS in water, aS and 10% (v/v) crowders in water and aS with 50 mM NaCl in water. For each scenario a trajectory between the time 1.5-2.0 us has been provided in the zip file. Respective folders are 750, 750_crowders, 750_salted. The trajectory files have been named traj.xtc while the files containing information regarding the system energies, pressure and volume have been named traj.nrg.

Within each folder the initial configuration used to start the simulations, all run files required to perform MD using GROMACS from scratch has also been provided. The system topology files that have been used in this study has also been included in the respective directories. The file names are to some extent self explanatory to a person who uses GROMACS frequently. Kindly contact jmondal@tifrh.res.in for any further query or for request of additional data.