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Tubulin's response to external electric fields

A molecular dynamics study

Paper: Tubulin's response to external electric fields by molecular dynamics simulations

md

protein.pdb protein.psf
System pdb and psf after equilibration. Used in every run.

initial.*
Coorindates, velocities, and cell dimensions from the final frame of the equilibration run.

parameters/**
CHARMM36 parameter files.

The electric field parameter was turned on using eFieldOn and eField

set inputname       last_runs_name
set outputname      this_runs_name

# for the 10ns run during which the an EEF was applied
eFieldOn			yes
# for a 750 kV/cm EEF in the positive transverse direction
eField		        0.035826345822314 0.026219852770675 0.16659974853940

data

Trajectory data, used for analysis, is available at https://figshare.com/s/32bd5a62009f184ebd47

analysis

Representative VMD/tcl scripts for the analyses performed on the 50 ns trajectory files. The types of analyses, and the range of frames that were studied, are below:

  • rmsd (full 50ns)
  • rmsf (10 to 20ns)
  • dipole (full 50ns)
  • secondary_structure (10 to 20ns)
  • dimer_curvature (10 to 20ns)
  • dimer_stretch (10 to 20ns)
  • h1_b2_loop (5 to 10ns) (using the last 5ns of 10ns runs over several magnitudes)
  • deviation (last frame of EEF exposure)