GTP-in-Microtubule DFT Electron Density

Description

DFT electron density computed on molecular-dynamics-sampled geometries of GTP hydrolysis in microtubule proteins.

Data generated using the Gaussian Plane Waves DFT at the PBE/TZV2P/400Ry level by PySCF.

Each tar corresponds to one metadynamics run of GTP hydrolysis mediated by microtubule proteins. In each tar, each inter*.restart folder is one geometry sampled from MD, and in each folder,

rho_22.npy: DFT density in a.u.

grid_sizes_22.dat: shape of the density

energy_22.dat: DFT ground state energy in a.u.

box.dat: box size in angstrom

centered.xyz: geometry placed at the center of the box

Example of reading the density in Python:

import numpy as np

rho = np.load("rho_22.npy")

rho = rho.reshape(*np.loadtxt("grid_sizes_22.dat", dtype=int))

External Files

Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/v5tec-g6p43/

Additional details