Hybrid Quantum-Classical simulations (QM/MM) with CP2K interface¶

In a molecular mechanics (MM) force field, the influence of electrons is expressed by empirical parameters that are assigned on the basis of experimental data, or on the basis of results from high-level quantum chemistry calculations. These are valid for the ground state of a given covalent structure, and the MM approximation is usually sufficiently accurate for ground-state processes in which the overall connectivity between the atoms in the system remains unchanged. However, for processes in which the connectivity does change, such as chemical reactions, or processes that involve multiple electronic states, such as photochemical conversions, electrons can no longer be ignored, and a quantum mechanical description is required for at least those parts of the system in which the reaction takes place.

One approach to the simulation of chemical reactions in solution, or in enzymes, is to use a combination of quantum mechanics (QM) and molecular mechanics (MM). The reacting parts of the system are treated quantum mechanically, with the remainder being modeled using the force field. The current version of GROMACS provides an interface to the popular Quantum Chemistry package CP2K 188.

Overview¶

GROMACS interactions between the QM and the MM subsystems are handled using the GEEP approach as described by Laino et al. 189. This method of evaluating interactions between the QM and MM subsystems is a variant of the “electrostatic embedding” scheme. The electrostatic interactions between the electrons of the QM region and the MM atoms and between the QM nuclei and the MM atoms are explicitly included into the Hamiltonian for the QM subsystem:

$H^{QM/MM} = H^{QM}_e-\sum_i^n\sum_J^M\frac{e^2Q_J}{4\pi\epsilon_0r_{iJ}}+\sum_A^N\sum_J^M\frac{e^2Z_AQ_J}{e\pi\epsilon_0R_{AJ}},$

where $$n$$ and $$N$$ are the number of electrons and nuclei in the QM region, respectively, and $$M$$ is the number of charged MM atoms. The first term on the right hand side is the original electronic Hamiltonian of an isolated QM system. The first of the double sums is the total electrostatic interaction between the QM electrons and the MM atoms. The total electrostatic interaction of the QM nuclei with the MM atoms is given by the second double sum. An important advantage of using the CP2K/GEEP combination is that it allows evaluation of forces for both QM-QM and QM-MM interactions, in the case of systems with periodic boundary conditions (PBC). To avoid double accounting for electrostatic interactions and LJ, classical MM charge on the QM atoms are zeroed out as well as LJ interactions between QM-QM atoms are excluded. It should be noted that LJ interactions between QM-MM atoms are kept and still calculated by GROMACS. Bonded interactions between QM and MM atoms are described at the MM level by the appropriate force-field terms. All bonds, consisting of 2 QM atoms, angles and settles containing 2 or 3 QM atoms, dihedrals containing 3 or 4 QM atoms are excluded from the forcefield evaluation. Broken chemical bonds between QM and MM subsystems needs to be capped in the QM calculation. This is done within CP2K by adding a hydrogen atom to complete the valence of the QM region. The force on this atom, which is present in the QM region only, is distributed over the two atoms of the bond. The cap atom is usually referred to as a link atom. Within the interface all described topology modifications are performed automatically during gmx grompp pre-processing.

Software prerequisites¶

CP2K version 8.1 (or later) should be linked into GROMACS as libcp2k. For a specific installation instructions please follow the Building with CP2K QM/MM support guide.

Limitations in simulation techniques¶

The QM/MM interface limits simulations in two ways. First, no topology modifications are possible during the simulations in the QM region. Second, interface completely ignores “B” state parameters in the topology, making double topology setups impossible, e.g. free-energy perturbation simulations (Free energy implementation).

In addition it should be noted that the contribution of forces from QM/MM to the system virial are not accounted for. The size of the effect on the pressure-coupling algorithm grows with the total summed force due to QM-MM interactions and might produce artifacts in simulations with the NPT ensemble.

Usage¶

QM/MM simulations with CP2K interface are controlled by setting mdp file options and, in some cases, providing an additional input file for gmx grompp with the -qmi command-line option. All options that are related to QM/MM simulations with CP2K are prefixed with qmmm-cp2k.

Setting qmmm-cp2k-active=true will trigger a QM/MM simulation using the whole system as QM part and default parameters for all other options.

Choosing atoms for QM calculation¶

The QM part of your system is chosen with a name that corresponds to an atom group in the index file of GROMACS to the qmmm-cp2k-qmgroup option in mdp file. The typical QM part should consist of atoms that are interesting from the chemical point of view, i.e. part of the system where reaction happens. To make computation of the QM part feasible, it should be small and as compact as possible in a space. DFT simulations often scale as 3rd order of the number of atoms in the QM part. This means increasing number of atoms in the QM part by a factor of 2 will slow down the simulation by a factor of 8.

In addition user should provide total charge of your QM subsystem with qmmm-cp2k-qmcharge option and spin-state (multiplicity) with qmmm-cp2k-qmmultiplicity option.

Supported QM methods¶

The QM method is chosen with qmmm-cp2k-qmmethod in the mdp file. Currently the following QM methods are supported:

1. qmmm-cp2k-qmmethod=PBE - DFT using PBE functional and DZVP-MOLOPT basis set.

2. qmmm-cp2k-qmmethod=BLYP - DFT using BLYP functional and DZVP-MOLOPT basis set.

That list will be updated with a new methods once they are tested and included into the interface.

Providing your own CP2K input file¶

In addition it is possible to use custom external CP2K input file with qmmm-cp2k-qmmethod=INPUT and providing file with gmx grompp with -qmi option. The external file will be incorporated into the tpr file of the simulation and are subject to the following restrictions:

1. RUN_TYPE option in the CP2K input should be equal to ENERGY_FORCE.

2. CHARGE option should be present.

3. MULTIPILICTY option should be present.

4. COORD_FILE_NAME option should be present pointing towards pdb file.

5. Both CHARGE_EXTENDED TRUE and COORD_FILE_FORMAT PDB options should be present.

6. Incremental includes (@INCLUDE directive) are not allowed in the CP2K input file .

Changing names of CP2K files¶

During gmx mdrun simulation additional files will be produced with .inp, .out and .pdb. They contain CP2K input, CP2K output and pdb file with point charges of MM atoms in the extended beta field. By default all CP2K related files names will be deduced from tpr simulation file name by adding _cp2k suffix. In order to change it manually qmmm-cp2k-qmfilenames option should be used.

Output¶

The energy output file will contain an additional “Quantum En.” term. This is the energy that is added to the system from the QM/MM interactions. In addition, a file containing CP2K output will appear in the simulation directory with the .out extension.

Future developments¶

support of additional DFT methods will be added in the future, as well as semi-empirical and DFTB description of the QM subsystem will be allowed. Support of the multiple time-stepping approach to speed-up simulation will be added. Excited state simulations will be implemented with TD-DFT description of the wavefunction.