Biomolecular QM/MM with CP2K and GROMACS

This guide provides practical advice on how to use CP2K and the GROMACS-CP2K interface to perform QM/MM simulation of biomolecular systems.

For general methodological advice on QM/MM modelling & simulation of biomolecular systems, see our guide on Best Practices in QM/MM Simulation of Biomolecular Systems

Overview:

• QM/MM overview
  • Prepare system
  • Minimisation, Equilibration and Thermalisation
  • Select QM atoms
  • Run MM only in CP2K
  • Run a simple QM/MM calculation in CP2K
  • Run MD with CP2K

System preparation:

• System preparation
  • Getting to know your biological system
  • Preparing your PDB file
  • Preparing topology and coordinate files for CP2K
• Selecting QM atoms
  • Initial selection
  • Dealing with breaking bonds
  • Expanding or shrinking the QM region

Input preparation:

• CP2K MM setup
  • MM forcefields types in CP2K
  • Connectivity formats
  • Coordinate formats
  • Important MM input parameters
  • Troubleshooting
• QM treatment
  • Mechanics of a DFT calculation in CP2K
  • A basic QM input
  • Basis sets
  • XC functionals
  • Pseudopotentials
  • Dispersion corrections
  • Important QM input parameters
  • Troubleshooting
• CP2K QM/MM parameterisation
  • CP2K QMMM input format
  • Setting up QM atoms
  • Important QMMM input parameters
  • QMMM Cell
  • Dealing with the QM-MM boundary
• GROMACS/CP2K interface QM/MM parameterisation
  • Selecting QM atoms
  • Gromacs QM/MM input parameters
  • Using a CP2K input

Running:

• Building CP2K
  • Downloading CP2K
  • Set up environment
  • CP2K toolchain
  • Compiling CP2K
  • Building the interface
• Running QM/MM simulations
  • Running a CP2K standalone job
  • Running QM/MM simulations with the GROMACS/CP2K interface
  • Performance considerations
• Understanding the CP2K output
  • General Output
  • Output from an MD run
• CP2K Troubleshooting
  • Abort messages
  • CPASSERT failed messages
  • Runtime issues