The files available here are data for the tutorials presented in Building complex membranes with Martini 3

Tutorial_1.zip Building symmetric membranes.  Subfolders:

1.setup  This subfolder includes a README and bash scripts to show how to use insane to build a symmetric membrane and prepare its topology and index files provided in the “example_files” subfolder

2.simulate  This subfolder includes a README, all simulation parameter files (“.mdp”) for energy minimization, equilibration and production runs with Gromacs, and a bash script to show how to run the simulations

3.analyze  This subfolder includes a README and bash, Python and R scripts to carry out the analysis presented in the paper.

example_files  This subfolder includes the ready-to-use structure (symmetric-bilayer.gro), topology (symmetric-bilayer.top) and index (index.ndx) files for a 10 nm x 10 nm x 12 nm simuation box including a plasma membrane model composed of 8 different lipid types asymmetrically distributed across the leaflets in a 0.15M NaCl solution.

Tutorial_2.zip  Building asymmetric membranes.  Subfolders:

1.outer_sym_memb

2.inner_sym_memb

3.asym_memb

Each of these subfolders has the same 1.setup, 2.simulate, and 3.analyze folders that should be followed in the given order, as explained in the README files. Inside the “3.asym_memb/example_files” subfolder, the ready-to-use structure (asymmetric-bilayer.gro), topology (asymmetric-bilayer.top) and index (index.ndx) files can be found for a 10 nm x 10 nm x 12 nm simulation box including a plasma membrane model composed of 8 different lipid types asymmetrically distributed across the leaflets in a 0.15M NaCl solution.

Tutorial 3.zip  Building asymmetric membranes with proteins.  Subfolders:

1.setup_protein  This subfolder includes a README and a bash script to convert an all-atomistic protein structure (2rh1-glup122.pdb) to a Martini 3 coarse-grained representation.

2.setup_rest  This subfolder includes a README and bash scripts to show how to use insane to place the coarse-grained protein into a plasma membrane model with asymmetric lipid composition.  

3.simulate This subfolder includes a README, all simulation parameter files (“.mdp”) for energy minimization, equilibration and production runs with Gromacs and a bash script to show how to run the simulations

4.analyze  This subfolder includes a README and bash, Python and R scripts to carry out the analysis presented in the paper.

Tutorial 4.zip  Building curved membranes  Subfolders:

1.ref_memb  This folder includes subfolders as explained in the paper to set up and simulate the flat membrane that will be used as a reference for the curved membrane.

2.curved_memb  This folder includes subfolders as explained in the paper to set up and simulate the curved membrane.

3.analyze  This folder includes all files necessary to analyze the curved membrane as explained in the paper.

 

Martini 3 force field parameters can be found upon release on github.com/Martini-Force-Field-Initiative/M3-Lipid-Parameters.

 

Copyright (c) 2024, Lawrence Livermore National Security, LLC. 
Produced at the Lawrence Livermore National Laboratory 
Written by Melanie König (m.konig@rug.nl) and Tugba N. Ozturk (ozturk1@llnl.gov).
Release number LLNL-MI-862719. 
All rights reserved.

This work was produced under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

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