GROMACS Guide

What is GROMACS?

GROMACS is a software suite for preparing, running, and analyzing molecular dynamics simulations.

Beginner Tutorial (Uses Older Versions of GROMACS)

If you are new to GROMACS, we recommend starting with this tutorial created by GROMACS developers which will acquaint you with the software suite and general workflow of running MD simulations without having to type any commands yourself. There are several ways to do this tutorial but we recommend selecting the option to run the tutorial online at MyBinder.org.

This tutorial will allow you to set up, visualize, and run your first MD simulation while also providing helpful tips and explanations about each step along the way. This tutorial should take a couple hours.

Intermediate Tutorials

After completing the online tutorial, it might be helpful to start digging into tutorials where you write the commands yourself. To do so, you’ll first need to start an interactive session on the HPC. Here are the general instructions to do that.

First, open up a terminal and login to the cluster. Replace where it says netID with your netID.

ssh -Y netid@hpc2.storrs.hpc.uconn.edu

If prompted, enter the normal password you use with your netID. Then, start an interactive session.

srun -N 1 -n 8 -p general --constraint=skylake --pty bash

Next, we can load the modules we’ll need.

module purge
module load slurm/slurm/21.08.8 gromacs/2022.3/gpu

Next let’s make a folder to store our files for this tutorial. We’ll start with tutorial 1 but you could do the same for any tutorial.

cd ~
mkdir gmx_tutorial_one

With GROMACS loaded, you’re much closer to starting these intermediate tutorials. There are a few steps where you will need to download files to be used during the tutorial. Since we’re doing this tutorial on the Storrs HPC, that means you’ll need to download the files and then upload them to the Storrs HPC. Once we download a file, we will then want to copy it to the HPC. One could use a service like Globus or FileZilla, but if you don’t have those you can easily copy the file using the scp command. First open a terminal and find where the file is. A good place to start looking is your Downloads folder.

cd ~/Downloads
ls

Once you find the file, then you can then use the scp command to copy the file to the HPC. Replace netid with your netID and name_of_file.ext with the name and file extension of the file you’re interested in copying to the HPC (e.g., ions.mdp).

scp name_of_file.ext netid@hpc2.storrs.hpc.uconn.edu:~/gmx_tutorial_one

If prompted, enter your password. Once the file says that it’s been 100% copied, then you’ll be able to find that file in the gmx_tutorial_one folder in your home directory on the cluster.

With that information, you’ll be able to approach the intermediate tutorials. Below are a list of free online tutorials for using GROMACS. Good luck!

MDTutorials for GROMACS

• Tutorial 1: Lysozyme in Water

• Tutorial 2: KALP₁₅ in DPPC

• Tutorial 3: Umbrella Sampling

• Tutorial 4: Biphasic Systems

• Tutorial 5: Protein-Ligand Complex

• Tutorial 6: Free Energy of Solvation

• Tutorial 7: Virtual Sites

Happy modeling!

~

Storrs HPC

hpc@storrs.uconn.edu