This directory contains the simulation trajectories for the Tead4 double motif bound to two Tead4 proteins.
Files in each directory:
* notes.txt gives the sequence that was used to build the simulation system, and any other remarks.
* comb.inpcrd, comb.pdb, and comb.prmtop give the initial configuration of the whole (hydrated) system. This is the starting point of our simulations.
* deh.inpcrd, deh.prmtop, and deh.dcd give the dehydrated trajectory. deh.inpcrd is at the start of the simulation, and deh.dcd covers the production run.
* ends.col is the colvar definition file, used to restrain the ends of the DNA and prevent fraying.
* makeStructure.leap is the file used by tleap (in the AmberTools package) to build the structure.
* all .namd files give the simulation parameters used for minimization, thermalization, equilibration, and production.

The original, fully-hydrated trajectory files are archived at Stowers and are available upon request.

The scripts directory contains several analysis scripts that were used to generate plots for the publication.

The wild_type directory additionally contains the protein PDB structure and an example of the B-form DNA generated by Avogadro that was used to build the simulation systems.