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

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.

Description of the data and file structure

The data are deposited as a .tar.gz file: it can be unpacked by running tar -xzvf traj-data.tar.gz.

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.

The parameter file is civsd-amber-top.parm7 and the topology files with and without
the waters/lipids are civsd.psf and civsd-pro.psf

Sharing/Access information

Derived data (collective variables computed from the raw trajectories) are available as supplementary information to the accompanying publication.

Code/Software

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 https://github.com/dinner-group/ci-vsd.