# AdK Gromacs Tutorial¶

Gromacs: aiming for 2018 (maybe will work for 5.x, 2016) 2.0.2 Jul 03, 2018

Warning

This tutorial was originally based on an older tutorial for Gromacs 4.x and has not been completely transitioned to modern Gromacs versions. It will not work seamlessly and a number of MDP options are outdated and need to be updated. Please raise any problems in the issue tracker.

Justin Lemkul’s excellent GROMACS Tutorials, which have recently been updated for Gromacs 2018.

## Objective¶

Perform an all-atom molecular dynamics (MD) simulation—using the Gromacs MD package—of the apo enzyme adenylate kinase (AdK) in its open conformation in a physiologically realistic environment, and carry out a basic analysis of its structural properties in equilibrium.

## Tutorial files¶

All of the necessary tutorial files can be found on GitHub in the Becksteinlab/AdKGromacsTutorial/tutorial directory, which can be easily obtained by git-cloning the repository:

git clone https://github.com/Becksteinlab/AdKGromacsTutorial.git


## Workflow overview¶

For this tutorial we’ll use Gromacs (versions 5, 2016, 2018 should work) to set up the system, run the simulation, and perform analysis. An initial structure is provided, which can be found in the tutorial/templates directory, as well as the MDP files that are necessary for input to Gromacs. The overall workflow consists of the following steps: