Coarse-grained Model of Titrating Peptides Interacting with Lipid Bilayers

This repository contains Jupyter Notebooks and simulation data for reproducing the work of the scientific paper Coarse-grained Model of Titrating Peptides Interacting with Lipid Bilayers, DOI:10.1063/1.5058234.

Layout

• Simulate.ipynb Jupyter Notebook to launch Wang–Landau Monte Carlo simulations using Faunus
• AAdensity.ipynb Jupyter Notebook to calculate and plot cross-sectional 2D density distributions from all-atom trajectories
• CGdensity.ipynb Jupyter Notebook to calculate and plot cross-sectional 2D density distributions from coarse-grained trajectories
• Train.ipynb Jupyter Notebook to train the continuum model against coarse-grained free energy values
• Map.ipynb Jupyter Notebook to map all-atom models onto the coarse-grained model
• PMFs.ipynb Jupyter Notebook to plot PMFs of membrane translocation of mono-, di-, and tripeptides
• allatom/ Gromacs MD simulation data on the translocation of basic amino acids across lipid bilayers
• coarsegrained/ Faunus simulation data on the translocation of basic amino acids cross lipid bilayers

Usage

To open the Notebooks, install python via Miniconda and make sure all required packages are loaded by issuing the following terminal commands

    conda env create -f environment.yml
    source activate pepmem
    jupyter-notebook