Data from the manuscript: Exploring the stereochemistry-specific tendency for interdigitation in synthetic monomycoloyl glycerol analogs through molecular dynamics simulations
DOI10.5281/zenodo.11090144Zenodo11090144MaRDI QIDQ6697862FDOQ6697862
Dataset published at Zenodo repository.
Camilla Foged, Artturi Koivuniemi, Suvi Heinonen, Matthew Davies, Alex Bunker, Mikko Karttunen
Publication date: 30 April 2024
Copyright license: Creative Commons Attribution 4.0 International
Data from the article "Exploring the stereochemistry-specific tendency for interdigitation in synthetic monomycoloyl glycerol analogs through molecular dynamicssimulations" Suvi Heinonen, Artturi Koivuniemi, Matthew Davies, Mikko Karttunen, Camilla Foged, and Alex Bunker 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
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