Data from the manuscript: Machine learning reveals structural characteristics of stereochemistry-specific interdigitation of synthetic monomycoloyl glycerol analogs

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

四种膜构型如下：
1. single = 单双层膜（single bilayer）：包含512个MMG分子与25600个水分子
2. db_large = 大型双双层膜（large double bilayer）：包含1024个MMG分子与51200个水分子
3. id_small = 小型插指型双双层膜（interdigitated double bilayer）：包含256个MMG分子与12800个水分子
4. db_small = 小型双双层膜（small double bilayer）：包含256个MMG分子与12800个水分子

每种膜构型对应两种MMG类似物：
1. MMG1：即MMG-1，为(2R,3S)/(2S,3R)构型立体异构体的1:1外消旋混合物
2. MMG6：即MMG-6，为(2R,3R)/(2S,3S)构型立体异构体的1:1外消旋混合物

文件名说明：
每个轨迹文件夹包含初始结构、输入结构文件、轨迹文件、能量文件与体系拓扑文件。此外，.mdp文件与拓扑文件存储于各自专属文件夹中。
- start.gro：能量最小化前的初始结构
- eq.gro：生产模拟的输入结构文件
- eq.cpt：平衡模拟检查点文件
- run.gro：最终帧结构文件
- run.cpt：生产模拟检查点文件
- run.tpr：生产模拟TPR文件
- run.xtc：生产模拟轨迹文件，包含最后500 ns的模拟数据
- run.edr：生产模拟能量文件，包含最后500 ns的模拟能量数据

注：大型双双层膜（db_large）体系基于已平衡的小型双双层膜（db_small）体系构建，因此其初始结构为平衡前的结构。

MDP文件说明：
分子动力学参数文件可于专属文件夹05_mdps/中获取，其中包含适用于所有体系的能量最小化、平衡模拟与生产模拟的参数文件：
- em1_charmm36.mdp：首次能量最小化参数文件（适用于所有体系）
- em_charmm36.mdp：二次能量最小化参数文件（适用于所有体系）
- eq1_noposres_charmm36.mdp：无位置约束的平衡模拟参数文件（适用于单双层膜体系single）
- eq1_posresin_charmm36.mdp：Z方向O1原子受约束的平衡模拟参数文件（适用于db_large、id_small、db_small体系）
- production_charmm36.mdp：生产模拟参数文件（适用于所有体系）

拓扑与位置约束文件说明：
每种MMG类似物的体系拓扑文件可于对应专属文件夹06_top/MMG1/、06_top/MMG6/中获取。分子拓扑文件、力场参数与位置约束文件则分别存储于子文件夹06_top/MMG1/topol/与06_top/MMG6/topol/中。

MMG-1相关文件：
- db_large-MMG1.top：MMG-1大型双双层膜体系拓扑文件
- db_small-MMG1.top：MMG-1小型体系拓扑文件，涵盖插指型与非插指型双双层膜
- single-MMG1.top：MMG-1单双层膜体系拓扑文件
- forcefield.itp：力场参数文件
- TIP3_CHARMM36.itp：水模型文件
- MMG1_2R3S_outer.itp：外层膜2R3S构型MMG-1分子拓扑文件
- MMG1_2S3R_outer.itp：外层膜2S3R构型MMG-1分子拓扑文件
- MMG1_2R3S_inner.itp：内层膜2R3S构型MMG-1分子拓扑文件
- MMG1_2S3R_inner.itp：内层膜2S3R构型MMG-1分子拓扑文件
- posres_MMG1_tail_z.itp：MMG-1分子尾部Z方向位置约束文件
- posres_MMG1_O1_z.itp：MMG-1分子头部基团O1原子Z方向位置约束文件

MMG-6相关文件：
- db_large-MMG6.top：MMG-6大型双双层膜体系拓扑文件
- db_small-MMG6.top：MMG-6小型体系拓扑文件，涵盖插指型与非插指型双双层膜
- single-MMG6.top：MMG-6单双层膜体系拓扑文件
- forcefield.itp：力场参数文件
- TIP3_CHARMM36.itp：水模型文件
- MMG6_2S3S_outer.itp：外层膜2S3S构型MMG-6分子拓扑文件
- MMG6_2R3R_outer.itp：外层膜2R3R构型MMG-6分子拓扑文件
- MMG6_2S3S_inner.itp：内层膜2S3S构型MMG-6分子拓扑文件
- MMG6_2R3R_inner.itp：内层膜2R3R构型MMG-6分子拓扑文件
- posres_MMG6_tail_z_2R3R.itp：2R3R构型MMG-6分子尾部Z方向位置约束文件
- posres_MMG6_tail_z_2S3S.itp：2S3S构型MMG-6分子尾部Z方向位置约束文件
- posres_MMG6_O1_z.itp：MMG-6分子头部基团O1原子Z方向位置约束文件