CP2K MM setup

An example CP2K input for a simple single energy MM calculation is shown below. Note that the RUN_TYPE is set to ENERGY and the METHOD in the FORCE_EVAL section is set to FIST for an MM run. This stands for Frontiers in Simulation Technology which is the method used in CP2K MM calculations.

&GLOBAL
   PROJECT project_name
   RUN_TYPE ENERGY
   PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
   METHOD FIST                       ! Do MM
   &MM
     &FORCEFIELD
     PARMTYPE AMBER                  ! use the Amber forcefield type (see also MM forcefields types in CP2K)
     DO_NONBONDED .TRUE.             ! short range non bonded interactions
     PARM_FILE_NAME ff_name          ! forcefield filename
     &SPLINE
        EMAX_SPLINE 1.0E04           ! max spline
        RCUT_NB [angstrom] 12        ! Cutoff radius for nonbonded interactions
     &END SPLINE
     &END FORCEFIELD
     &POISSON
        &EWALD
           EWALD_TYPE SPME           ! recommended ewald type
           GMAX 70                   ! number of grid points 1 per angstrom in each direction
        &END EWALD
     &END POISSON
   &END MM
   &SUBSYS
      &CELL
        ABC x y z                    ! size in x,y,z in Angstrom
        PERIODIC XYZ
        ALPHA_BETA_GAMMA 90 90 90    ! cubic cell (90 degrees between alpha, beta, gamma)
      &END CELL
      &TOPOLOGY
         CONN_FILE_FORMAT AMBER      ! use the Amber format (see also MM forcefields types in CP2K)
         CONN_FILE_NAME ff_name      ! amber forcefield filename
         COORD_FILE_FORMAT PDB       ! coords in pdb formant (see also Coordinate formats)
         COORD_FILE_NAME coord_name  ! coordinate filename
      &END TOPOLOGY
   &SUBSYS
&END FORCE_EVAL

The MM and SUBSYS sections of FORCE_EVAL are required for this calculation. The MM section contains all the parameters related to the atomic interations such as the forcefield, and Poisson solver and splines used in the non-bonded interations. The SUBSYS section contains the systems topology information such as the atomic coordinates, the cell size and the connectivity.

MM forcefields types in CP2K

Amber

If using an Amber forcefield the .prmtop file should be used as the forcefield file PARM_FILE_NAME in the FORCEFIELD section and as the connectivity file CONN_FILE_NAME in the TOPOLOGY section. Both the PARMTYPE and CONN_FILE_FORMAT should be set to AMBER.

CHARMM

The CHARMM force field (i.e. a .prm file) can be used by setting PARMTYPE to CHM. The psf CHARMM connectivity file is used with CONN_FILE_FORMAT set to PSF. Example usage can be found in this tutorial.

GROMOS

The GROMOS 96 format can be used by specifying PARMTYPE G96.

Connectivity formats

AMBER - Use AMBER topology file .prmtop or .top
G87 - Use GROMOS G87 topology file.
G96 - Use GROMOS G96 topology file.
PSF - Use a CHARMM PSF file.
UPSF - Use an unformatted PSF file.

Coordinate formats

The atomic coordinates are supplied in the topology section. The following different file types are allowed.

CIF - Coordinates provided through a CIF (Crystallographic Information File) file format
CRD - Coordinates provided through an AMBER file format e.g. .inpcrd .crd
G96 - Coordinates provided through a GROMOS96 file format
PDB - Coordinates provided through a PDB file format
XTL - Coordinates provided through a XTL (MSI native) file format
XYZ - Coordinates provided through an XYZ file format

Note that even if your coordinates file contains information about the box dimensions these should be listed in the cp2k input in the CELL section.

Important MM input parameters

EMAX_SPLINE

Specifies the maximum value of the potential up to which splines will be constructed

RCUT_NB

Cutoff radius for nonbonded interactions. This value overrides the value specified in the potential definition and is global for all potentials.

EWALD_TYPE

This parameter specifies the type of non-bonded long-range interaction method should be used in the calculation. The following options are available.

NONE - standard real-space coulomb potential is computed together with the non-bonded contributions
EWALD - standard non-fft based ewald
PME - particle mesh using fft interpolation
SPME - smooth particle mesh using beta-Euler splines (recommended)

GMAX

Number of grid points (SPME and EWALD). Supply a single value N for all three dimensions or Nx, Ny, Nz for individiual dimensions. One grid point per Angstrom is a typical chocie, however such a value may cause the calculation to become too slow for large cells.

Troubleshooting

GEOMETRY wrong or EMAX_SPLINE too small!

This is usually means there is a problem with the MM forcefield or the geometry of your system.

KIND not found

You may get an error message from CP2K saying "Unknown element for KIND". This happens when a symbol that does not match a proper element is found in the coordinate and force field files. The workaround for this is to let CP2K know what element the offended symbol should correspond to. This is done by adding in the SUBSYS section a new KIND section for the novel symbol where to specify the element via the keyword ELEMENT. Alternatively, one can specify the element symbol in the PDB coordinate file.