Tutorial: Simulating AdK with Gromacs

Objective: Perform a MD simulation of the the enzyme adenylate kinase (AdK) in its open conformation without a ligand bound. Simulate it in a realistic environment (100 mM NaCl solution at \(T = 300\) K and \(P = 1\) bar) and analyze its structural properties.

For this tutorial we use Gromacs (version 4.5.5) to set up the system, run the simulation, and perform analysis. The overall workflow contains the following steps:

1. Download tutorial files and organize the work space
2. Setup
   • obtain structure 4AKE from PDB, select chain A
   • use default protonation states
   • generate topology
   • solvate in water in simulation cell (rhombic dodecahedron)
   • add NaCl ions to neutralise and final physiological concentration of 100 mM
3. Energy minimisation (EM)
4. Position restraint equilibration of solvent (MD); NPT (use weak coupling (Berendsen) schemes)
5. Equilibrium MD simulation (unrestrained, NPT, use Nose-Hoover and Parrinello-Rahman temperature and pressure coupling)
6. Analysis
   • RMSD
   • RMSF
   • opening (NMP-LID distance)
   • radius of gyration
   • secondary structure

All input files are provided in the tar file AdKTutorial.tar.bz2. Start by downloading and uncompressing the file:

curl -O http://becksteinlab.physics.asu.edu/pages/courses/2013/SimBioNano/13/AdKTutorial.tar.bz2
tar -jxvf AdKTutorial.tar.bz2
cd AdKTutorial

A starting structure can be found in the AdKTutorial/coord directory and MDP files are in AdKTutorial/templates.

Then work through the individual steps of the workflow:

Steps of the workflow

• 1. Directory organization
• 2. Setup of the solvated protein system
• 3. Energy minimization
• 4. Position restraints MD
• 5. Equilibrium molecular dynamics
• 6. Analysis

Indices and tables

• References
• Search Page