AdK Gromacs Tutorial

Gromacs:5.x, 2016, 2018 Tutorial:2.0.1 Date:Jul 03, 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:

• 1. Directory organization
• 2. Generate a solvated protein system
• 3. Energy minimization
• 4. Position-restrained equilibration
• 5. Equilibrium molecular dynamics
• 6. Trajectory visualization
• 7. Analysis
• 8. References