Input Data for "Assembly and Analysis of Cell-Scale Membrane Envelopes"

Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar command: `tar -zcvf protocellmodeling.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*trr" --exclude="*js" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*state_prev.cpt" --exclude="*.o[0-9]*" cgDracula`, which intentionally excludes large files. The full 4.8TB dataset that includes trajectories is available upon request.

The data is split into multiple subdirectories and largely undocumented, however here are the highlights:

The Analysis subdirectory is where the analysis in the paper lives. All other directories are related to building or running systems.

getsources.py in the main directory is the script that downloads the initial structure from MemProtMD.

transform.py builds the initial protein models from MemProtMD.

vesiclebuilder.py builds the lipid ball.

protpatchplacer.py sets up the ultra-coarse grained simulation, which is in the supercg directory.

movepatches.py takes the results from the ultra-coarse grained simulation, and builds the protein ball.

gendx.tcl generates the density maps from the protein ball.

This is used in lipids/picklipids.py, which cuts out the pieces of the lipid that need to be removed.

The water is added to the system with addwater/quicksolvate.sh

The system is ionized by ionize.py

And a topology is written by writetop.py