DOI: 10.5281/zenodo.11090144
title: Data from the manuscript: Machine learning reveals structural characteristics of stereochemistry-specific interdigitation of synthetic monomycoloyl glycerol analogs

description: Four membrane configurations:

1. single = single bilayer (512 MMG molecules and 25600 water molecule) 2. db_large = large double bilayer (1024 MMG molecules and 51200 water molecules)3. id_small = interdigitated double bilayer (256 MMG molecules and 12800 water molecules)4. db_small = small double bilayer (256 MMG molecules and 12800 water molecules)

Each membrane configuration has 2 different MMG analogs:

1. MMG1 = MMG-1, 1:1 racemic mixture of stereoisomers with (2R,3S)/(2S,3R) configurations2. MMG6 = MMG-6, 1:1 racemic mixture of stereoisomers with (2R,3R)/(2S,3S) configurations

File names:

Each trajectory folder contains starting structures, input structure files, trajectory, energy file and system topology file.Additionally, the .mdp files and topologies are located in their own folders.

-  start.gro    = starting structure before energy minimization**-  eq.gro    = input structure file for production-  eq.cpt    = equilibration checkpoint file-  run.gro    = final frame structure file-  run.cpt    = production checkpoint file-  run.tpr    = production tpr file - run.xtc    = production trajectory file, final 500 ns-  run.edr    = production energy file, final 500 ns

the db_large system is built with equilibrated db_small system, hence the starting structure is before the equilibration.

MDP-files:

Molecular dynamics parameter files can be found in their own folder (05_mdps/). Files for energy minimization,equilibration and production run are provided.

- em1_charmm36.mdp        = 1st energy minimization (for all systems)- em_charmm36.mdp        = 2nd energy minimization (for all systems)- eq1_noposres_charmm36.mdp    = equilibration without position restraints (for single)- eq1_posresin_charmm36.mdp    = equilibration with O1 atoms constrained in Z-direction (for db_large, id_small, db_small)- production_charmm36.mdp    = production run (for all systems)

Topologies and position restraint files:

System topologies for each MMG analog can be found in their own folders (06_top/MMG1/, 06_top/MMG6/). Molecular topologies, forcefield parameters and position restraint files can be found from their respective folders (06_top/MMG1/topol/, 06_top/MMG6/topol/).

MMG-1:

- db_large-MMG1.top        = MMG-1 large double-bilayer system- db_small-MMG1.top        = MMG-1 small systems: interdigitated and non-interdigitated double bilayers            - single-MMG1.top            = MMG-1 single bilayer system- forcefield.itp         = force field parameters- TIP3_CHARMM36.itp        = water model- MMG1_2R3S_outer.itp         = outer leaflet 2R3S MMG-1      - MMG1_2S3R_outer.itp         = outer leaflet 2S3R MMG-1   - MMG1_2R3S_inner.itp          = inner leaflet 2R3S MMG-1- MMG1_2S3R_inner.itp         = inner leaflet 2S3R MMG-1- posres_MMG1_tail_z.itp        = position restraints on MMG tails in z-direction- posres_MMG1_O1_z.itp         = position restraints on MMG headgroup O1 atom in z-direction

MMG-6:

- db_large-MMG6.top        = MMG-6 large double-bilayer system- db_small-MMG6.top        = MMG-6 small systems: interdigitated and non-interdigitated double bilayers- single-MMG6.top        = MMG-6 single bilayer system- forcefield.itp                = force field parameters- TIP3_CHARMM36.itp             = water model- MMG6_2S3S_outer.itp           = outer leaflet 2S3S MMG-6  - MMG6_2R3R_outer.itp           = outer leaflet 2R3R MMG-6- MMG6_2S3S_inner.itp           = inner leaflet 2S3S MMG-6- MMG6_2R3R_inner.itp           = inner leaflet 2R3R MMG-6 - posres_MMG6_tail_z_2R3R.itp    = position restraints on tails in z-direction                                                            - posres_MMG6_tail_z_2S3S.itp    = position restraints on tails in z-direction- posres_MMG6_O1_z.itp        = position restraints on MMG headgroup O1 atom in z-direction