Raw data of the molecular dynamics simulation trajectories and normal mode analyses of tubulin heterodimer A2205

This dataset contains data from molecular dynamics (MD) simulations and normal mode analysis (NMA) performed on tubulin protein.\nMD_parameters-structure.zip: Tubulin_dimer_model.pdb containing tubulin structure, .mdp files containing parameters for MD simulation and MD.xtc file containing the trajectory of 500ns long MD simulation. \nNMA_parameters-structures.zip: .mdp files containing parameter files for NMA and five structure files as an example of each type of system containing protein with different water layers as .pdb files. \nNMA was performed on five types of systems, containing different water shells around protein: protein with - no water, 3?, 5?, 8?, and 10? of water. One hundred calculations were performed for each type of system above. Results obtained and analyzed in NMA calculations are provided here: frequency and eigenvectors for first one thousand eigenmodes for each NMA calculation.\nfrequency_files.zip: contains five folders named as frequency_0A, frequency_3A, frequency_5A, frequency_8A, and frequency_10A for systems with no water, 3?, 5?, 8?, and 10? water layer around protein. Each of these folders contain one hundred .xvg files with frequencies of normal modes. \neigenvec-files_0A.zip: one hundred .trr files containing first one thousands eigenmodes obtained from NMA for systems with only protein (i.e. no water). \neigenvec-files_3A.zip: one hundred .trr files containing first one thousands eigenmodes obtained from NMA for systems with 3? water layer around protein. \neigenvec-files_5A|_p1.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 5? water layer around protein. \neigenvec-files_5A|_p2.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 5? water layer around protein. \neigenvec-files_8A|_p1.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 8? water layer around protein. \neigenvec-files_8A|_p2.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 8? water layer around protein. \neigenvec-files_10A|_p1.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 10? water layer around protein. \neigenvec-files_10A|_p2.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 10? water layer around protein. \n\n