AdK Gromacs Tutorial

The full tutorial is available online through Read the Docs.

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 obtained by cloning the repository

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

Workflow overview

For this tutorial we'll use Gromacs (version 5.1.3) to set up the system, run the simulation, and perform analysis. An initial structure is provided, which can be found in the :file: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. Download tutorial files and set up working directories

   • Obtain structure 4AKE from PDB
   • Generate a stripped PDB file containing only chain A and no crystal waters

2. Solvate the protein system

   • Generate topology using default protonation states

   • Solvate in water in simulation cell (rhombic dodecahedron)

   • Ionize system with NaCl to neutralize and obtain physiological concentration

3. Perform energy minimization

4. Perform position-restrained equilibration

5. Run production MD in the NPT ensemble

6. Visualize the trajectory

   • Center the protein in a box with primitive unitcell representation (periodic boundary conditions)

   • RMS-fit the protein in each snapshot to the first snapshot