Dynamics and structural responses to cis-trans isomerization in bacterial lipid bilayers

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 cis-trans-membrane.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*log" --exclude="*xsc" --exclude="*coor" --exclude="*vel" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*ppm" --exclude="*png" --exclude="*pdf"  --exclude="*catchy*" --exclude="*svg" --exclude="*restart*" --exclude="*history" --exclude="core.*" --exclude="FFTW_NAMD*" --exclude="*avi" --exclude="*mp4"  --exclude="pressureprofile" --exclude="pressureprofile-npt" --exclude="pressureprofile-npt-iccer" --exclude="joshfiles" cis-trans-membrane which intentionally excludes large files. The full dataset that includes trajectories is available upon request.

The data is split into two directories initially "analysis" and "gen_mem"

analysis folder contains all the different analysis and ploting scripts used in the manuscript

gen_mem folder contains all the scripts for building the system and running the NAMD equilibration simulation and the lateral pressure profile simulation.