MM parameterisation

This section describes how to set up a QM/MM system when using the GROMACS-CP2K interface. It assumes that you have a equilibriated GROMACS coordinates file (.gro), a GROMACS topolopy file (.top) and a MD parameter file (.mdp) with settings to do a classical MM simulation. From this this guide will show you how to select your QM atoms, and set the parameters in order to run a QM/MM simulation.

Examples of input files for running QM/MM simulations with the GROMACS/CP2K interface can be found in the Bioexcel QM/MM benchmark suite.

Selecting QM atoms

The atoms for the QM region must be given through a GROMACS index file (.ndx). You can select a group of atoms and then name the group appropirately e.g. QMatoms.

For example to select all non-water atoms to be treated with QM:

gmx_mpi make_ndx -f ${INPUT}.gro


Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:     1      Other residues
There are:  2384      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...

0 System              :  7186 atoms
1 Other               :    34 atoms
2 Protein             :    34 atoms
3 Water               :  7152 atoms
4 SOL                 :  7152 atoms
5 non-Water           :    34 atoms


 nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups
 'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues
 't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help
 'r': residue              'res' nr         'chain' char
 "name": group             'case': case sensitive           'q': save and quit
 'ri': residue index

> name 5 QMatoms

This group name should then match the name set in the qmmm-cp2k-qmgroup name in the .mdp file. The index file will need to be provided in the grompp command.

Gromacs QM/MM input parameters

The main CP2K QMMM parameters for the QM/MM .mdp file are shown below:

; CP2K QMMM parameters
qmmm-cp2k-active              = true    ; Activate QMMM MdModule
qmmm-cp2k-qmgroup             = QMatoms ; Index group of QM atoms
qmmm-cp2k-qmmethod            = PBE     ; Method to use
qmmm-cp2k-qmcharge            = 0       ; Charge of QM system
qmmm-cp2k-qmmultiplicity      = 1       ; Multiplicity of QM system

qmmm-cp2k-active

Set to true to turn on QMMM.

qmmm-cp2k-qmgroup

The group name for the QM atoms as in the index file.

qmmm-cp2k-qmmthod

The method to use for the QM atoms. At present the available options are:

PBE - Use the PBE method in CP2K.
BLYP - Use the BLYP method in CP2K.
INPUT - pass your own CP2K input file contain the QM set up. See below.

Using a CP2K input

If the functional method you need is not available or if you wish to change any of the QM settings then you should provide your own CP2K input file.

The best way to generate this is to first run the inferface with either the PBE or BLYP option set to create a CP2K input file with the interface. You can then use this file as a template and edit it as you wish.

To use this CP2K input file rather than generate a new one you should set the qmmethod to INPUT in the .mdp file as shown below:

qmmm-cp2k-qmmethod            = INPUT    ; use own cp2k.inp

To generate the tpr file for running you also need to add the name of the cp2k input file with the -qmi option:

gmx grompp -f sys.mdp -p sys.top -c sys.gro -n sys.ndx -qmi sys_cp2k.inp -o sys.tpr

You may then run the .tpr as usual.