Simulation data for "Chain Sliding versus β-Sheet Formation upon Shearing Single α-Helical Coiled Coils"

Content - Input and output files of the steered molecular dynamics simulations; python, VMD/Tcl scripts to produce the figures containing simulation data presented in the main text and in the SI of the associated publication. Movies of two simulation runs of the A5N3B5N3 coiled coil at vpull=0.01 nm/ns: two movies of different durations of a simulation run where the alpha-to-beta transition occurs (A5B5_BetaSheet-1min30sec.gif and A5B5_BetaSheet-30sec.gif); one movie of a simulation run where the alpha-to-beta transition does not occur (A5B5_noBetaSheet-23sec.gif). The movies can be played by dragging-and-dropping into a web browser (e.g., Firefox). Instructions Usage of this dataset necessitates basic knowledge of python, LaTex, VMD/Tcl and Gromacs. Unzip all files in the same directory. - analysis05/dataverse-simulation-figures.pdf contains all figures with simulation data shown in the main text and in the SI of the associated publication. - analysis05/dataverse-simulation-figures.tex can be consulted to determine the names of each figure. With a few exceptions, any output files produced by a script share the same prefix as the script name. E.g., figure s027_v04_A4B4_vE-2_ForceTrace_vs_z-L0.pdf was produced by script s027_v04*py; vmd04_v01*.dat was produced by vmd04_v01*.tcl. The exceptions are the few figures that were produced interactively, and the output files of scripts vmd001_interchainHBs_*.tcl (because sometimes bad days happen, and imperfectly-named progress is better than no progress at all). - The simulation trajectories that gave origin to the simulation data presented in each figure can be identified from the input files listed within each script