Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations

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 terpenoidpermeability.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" Terpenoid-Permeability, which intentionally excludes large files. The full dataset that includes trajectories is available upon request.

The data is split into two directories initially "build" and "Simulations"

"build" directory is the part where initial system for unbiased and biased simulation were build using "resolvate.tcl" and "smd-single-build-system.tcl" respectively.

"Simulations" directory has the different namd files for running unbiased simulation, steered molecular dynamics and replica exchange  umbrella sampling.

The folder structure was generated using  "gendirs*.py".
The unbiased simulations were run using "run.namd".
Steered molecular dynamics namd files were with name "step*.namd" and colvars configuration file are named "step*.conf".

Replica exchange moleuclar dynamics (REUS) system was generated using "buildreplicas.tcl".
Replica windows size and  force constant were written into a namd configuration file using "reus-genscript.py".
REUS general configuration file containing the parameters and forcefield is  named as "base.namd".
Colvars for REUS are in "replicadistZcolvars.conf".
Umbrella sampling is performed with "umbrella.namd".