Dynamics of activation in the voltage-sensing domain of Ci-VSP

<p>This dataset contains unbiased molecular dynamics trajectories, stripped of water and lipid coordinates due to size constraints. It also contains full initial and final structures for all trajectories.</p><h3>Description of the data and file structure</h3><p>The data are deposited as a .tar.gz file: it can be unpacked by running tar -xzvf traj-data.tar.gz.</p><p>The trajectories are organized into two groups (group1 and group2), each containing a folder with stripped_trajs as .xtc files, as well as the full starting and ending coordinates (with waters and lipids) as intial_structs and final_structs. The models for the down--, down, up, and up+ states are in models.</p><p>The parameter file is civsd-amber-top.parm7 and the topology files with and without<br>the waters/lipids are civsd.psf and civsd-pro.psf</p><h3>Sharing/Access information</h3><p>Derived data (collective variables computed from the raw trajectories) are available as supplementary information to the accompanying publication.</p><h3>Code/Software</h3><p>Analysis of the trajectories can be performed using the MDAnalysis, MDTraj, PyEMMA, scikit-learn, and VMD, softwares along with custom codes written in Python/Jupyter notebooks and tcl. Custom codes are available at <a href="https://github.com/dinner-group/ci-vsd">https://github.com/dinner-group/ci-vsd</a>.</p>