MD in a membrane environment

Welcome to the repository for the 11/01/2024 and 16/01/2024 lectures on MD of bilayers and membrane proteins.

Distribution

Under theory/ you have the theoretical presentation to the topic. Under practical/ you have a protocol with the different steps to be followed to:

• Build, minimize, equilibrate, simulate and analyze a POPC membrane system (under just_popc/).
• Build and analyze a POPC+CHL membrane system (under popc+chl/).
• Build and analyze a POPC+CHL membrane system with an embedded membrane protein (under membrane_protein/).

Main software

• PACKMOL-memgen to build the systems.
• GROMACS to prepare, simulate and analyze the simulations.
• FATSLiM to analyze the membranes in the simulations.

Setting up

In this repo we assume the Anaconda package manager is installed in your computer (you can check that by typing conda on your terminal session). If you do, continue from Creating an environment. If not, go on with Installing miniconda.

Installing miniconda

A lighter version of Anaconda can be installed, and that is miniconda. To download and install it:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

Follow the instructions.

Once you have it installed, you probably have to restart your terminal or do source ~/.bashrc, and then conda init bash.

Creating an environment

Now we're going to create an environment and we're going to call it membranes:

conda create -n membranes python=3.6
conda activate membranes

And install all the packages needed through conda install:

conda install -c conda-forge numpy pandas matplotlib pytest ambertools

Say Y.

Installing the rest of the software

We might need to install the molecular dynamics machine as well. First check if it's installed in your system by typing gmx help or which gmx in your shell. If there's no prompt or the software is not installed, do:

sudo apt install gromacs

To install FATSLiM and test if it works:

pip install fatslim
fatslim self-test

To start working with the practical part, git clone this repo anywhere you want in your local machine and follow the steps of the protocol.