MD Simulations with Gromacs

Overview

This page is intended to serve as a resource for those interested in doing MD Simulations with Gromacs.

Set-Up

The first step is to download the Gromacs software. This can be done by navigating to the Gromacs Documentation page, found here and then clicking on Download under the most recent version. This one is currently 2019.1.

The next step is to click on the link next to "as http".

The installation guide can be found here. I provide this because this is a process that is operating system specific, so I will focus my Set-Up instructions for those that are working on Mac OS.

Now that you have hopefully downloaded a .tar of the Gromacs software, you will have to "unzip" the tar ball. This can be done by opening a terminal and typing the following:

    cd Downloads
    tar xfz gromacs-2019.tar

Note that the "gromacs-2019.tar" should reflect whatever the name of your downloaded file is. At this point, I would like to point out that you will need a compiler called Cmake in order to successfully install Gromacs. I was able to download this using Homebrew, which may or may not be possible for you. If you do not have homebrew, then you can download Cmake from this webpage!

    brew install cmake

Next, you navigate to the directory that you have just created by typing the following commands in sequential order:

    cd Gromacs-2019
    mkdir build
    cd build
    cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
    make
    make check
    sudo make install
    source /usr/local/gromacs/bin/GMXRC

Congratulations, you have successfully installed Gromacs onto your machine! (I hope...) If you encounter issues, refer back to the documentation, as common installation issues for all operating systems are addressed there!

To test your installation, go back to the terminal and type:

    gmx -version 

If you get some kind of error (i.e. command not found), then you should go back to the documentation. Otherwise, you are ready to get started!

Procedure

Here is a flowchart depicting the general procedure for running a GROMACS MD Simulation:

A flowchart for a typical GROMACS MD Simulation run of a protein in a box of water.

The first thing that we will do to see what GROMACS is capable of is follow a tutorial for KALP-15 in a DPPC bilayer. You can find a series of tutorials here!

Step 1: You need to get a .pdf file. You can get that file here.

Then, navigate to the directory where this is located. It is likely in your Downloads folder, so you can navigate there by typing the following command into the terminal window:

    cd Downloads

Then type the following into the terminal:

    gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc

Next, you should choose the GROMOS96 53A6 parameter set... This is done by typing the number in front of this set. For me, it was 13.

Choose none for both termini. This is done by typing the number in front of the "None" option. For me, this was 2. (twice)

Next, you will have to download the lipid parameter files titled:

• dppc128.pdb - the structure of a 128-lipid DPPC bilayer
• dppc.itp - the moleculetype definition for DPPC
• lipid.itp - Berger lipid parameters

and can be found here!