Dataset of "Martini 3 overestimates lipid scrambling by membrane proteins"

This repository contains the source data and simulation inputs used for “Martini 3 Overestimates Lipid Scrambling by Membrane Proteins.” Due to storage limitations, we provide the simulation input files, along with key GROMACS outputs, including structure files (.gro) from energy minimisation (em), equilibration (eq1 and eq2), and production molecular dynamics (MD), the strided trajectory .xtc files as well as the corresponding md.tpr files. These files should be sufficient to reproduce the simulation trajectories. If additional files are required, or for any questions related to this dataset, please feel free to contact the authors. Please see the paper for the methodological details. Contents and description scrambling_dataset.tar.gz (~1 GB) The dataset is organised using the following directory structure: /<forcefield_or_restraints>/<protein>/<prep_and_analysis> The dataset contains four top-level directories for main simulation conditions: Martini 2 (M2), Martini 3 (M3), Martini 3 modification (M3_modification) and experimental restraints (restraints) simulations . Within each of the four directories, a separate folder is provided for each protein. Each protein folder contains two subdirectories: prep and analysis. The prep subdirectory contains simulation input files including protein structure, topology, Parameter (.mdp) files etc. The analysis subdirectroy contains key simulation outputs including .gro files from energy minization (em), eqaulibration (eq1 & eq2) and production MD (md) and md.tpr file. Files with the suffix *-pm.gro contain only the protein and membrane (stripped of their water and ions). Strided_traj.tar.gz (~ 47GB) Due to storage limitations, this repository contains stripped and strided trajectories, including only the protein and membrane with every fifth frame retained. The dataset is organised into four main directories: Martini 2 (M2), Martini 3 (M3), Martini 3 modifications (M3_modification), and experimental restraint simulations (restraints). For the M2 and M3 directories, trajectory files follow the naming convention: <protein>-<forcefield>-<rep>-md-pm-strided.xtc For the M3_modification directory, trajectory files follow: <protein>-<modification>-<rep>-md-pm-strided.xtc For the restraints directory, trajectory files follow: <protein>-<restraint>-<rep>-md-pm-strided.xtc. Note that all scrambling analyses were performed using the original full trajectories. The stripped and strided trajectories were generated only for data upload and storage efficiency purposes.