Overview of the CP2K input
The CP2K input file, cp2k_qmmm_equil.inp, is divided in different sections that we will explain separately:
&GLOBAL section
It contains general information regarding which kind of simulation to perform.
&GLOBAL
PROJECT MD_QMMM ! Name of the calculation
PRINT_LEVEL LOW ! Verbosity of the output
RUN_TYPE MD ! Calculation type: MD
&END GLOBAL
&FORCE_EVAL section
It contains the parameters needed to calculate energy and forces and describe the system you want to analyze. It has several important subsections:
&DFT, which specifies the parameter needed by LCAO DFT programs
&FORCE_EVAL
METHOD QMMM ! Hybrid quantum classical
STRESS_TENSOR ANALYTICAL ! Compute the stress tensor analytically (if available).
&DFT ! Parameter needed by LCAO DFT programs
CHARGE 0 ! The charge of the QM system
&QS ! parameters needed to set up the Quickstep framework
METHOD PM3 ! Specifies the electronic structure method that should be employed
&SE ! Parameters needed to set up the Semi-empirical methods
&COULOMB ! parameters for the evaluation of the COULOMB term
CUTOFF [angstrom] 10.0
&END
&EXCHANGE ! parameters for the evaluation of the EXCHANGE and core Hamiltonian terms
CUTOFF [angstrom] 10.0
&END
&END
&END QS
&SCF ! Parameters needed to perform an SCF run
MAX_SCF 30 ! Maximum number of SCF iterations
EPS_SCF 1.0E-6 ! Target accuracy for the SCF convergence
SCF_GUESS ATOMIC ! initial guess for the wavefunction: Generate an atomic density using the atomic code
&OT ! options for the orbital transformation (OT) method
MINIMIZER DIIS ! Minimizer to be used with the OT method
PRECONDITIONER FULL_SINGLE_INVERSE
&END
&OUTER_SCF ! parameters controlling the outer SCF loop
EPS_SCF 1.0E-6 ! Target gradient of the outer SCF variables
MAX_SCF 10 ! Maximum number of outer loops
&END
&END SCF
&END DFT
&MM, which includes the parameters to run a MM calculation (such as the forcefield). Here we have to manually edit the &MM subsection PARM_FILE_NAME and add the modified topology name system_LJ_mod.parm7.
&MM ! Parameters to run a MM calculation
&FORCEFIELD ! Set up a force_field for the classical calculations
PARMTYPE AMBER
PARM_FILE_NAME system_LJ_mod.parm7
&SPLINE ! Parameters to set up the splines used in the nonboned interactions
EMAX_SPLINE 1.0E8 ! Maximum value of the potential up to which splines will be constructed
RCUT_NB [angstrom] 10 ! Cutoff radius for nonbonded interactions
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
! Ewald parameters controlling electrostatic
EWALD_TYPE SPME ! Type of ewald
ALPHA .40 ! Alpha parameter associated with Ewald (EWALD|PME|SPME)
GMAX 80 ! Number of grid points (SPME and EWALD)
&END EWALD
&END POISSON
&END MM
&SUBSYS, which specifies the information of the system: coordinates, topology, molecules and cell. Here we have to manually edit the following sections:
&CELLsubsection with the simulation box size: ABC and ALPHA_BETA_GAMMA.&TOPOLOGYsubsection with the Amber topology and coordinate files.- We must add any atomtype that CP2K doesn’t recognise such as the counterions (Na+ and NS atom type) and specify their element.
&SUBSYS ! a subsystem: coordinates, topology, molecules and cell
&CELL !Set box dimensions here
ABC [angstrom] XXX XXX XXX
ALPHA_BETA_GAMMA XXX XXX XXX
&END CELL
&TOPOLOGY ! Topology for classical runs
CONN_FILE_FORMAT AMBER
CONN_FILE_NAME system_LJ_mod.parm7
COORD_FILE_FORMAT CRD
COORD_FILE_NAME system.equil0.rst7
&END TOPOLOGY
!NA+ is not recognized by CP2K, so it is necessary to define it here using KIND
&KIND NA+
ELEMENT Na
&END KIND
&KIND NS
ELEMENT N
&END KIND
&END SUBSYS
&QMMM, which contains all the information on the QM/MM calculation. This includes the definition of QM region which we must specify manually.
We define the QM region here
&QMMM ! Input for QM/MM calculations
ECOUPL COULOMB ! type of the QM - MM electrostatic coupling
&CELL ! Set box dimensions here
ABC 40 40 40
ALPHA_BETA_GAMMA 90 90 90
&END CELL
&QM_KIND N ! N atoms in the QM region
MM_INDEX 1 10
&END QM_KIND
&QM_KIND O ! O atoms in the QM region
MM_INDEX 8
&END QM_KIND
&QM_KIND C ! C atoms in the QM region
MM_INDEX 2 3 4 5 6 7 9 11 12 13 14 15 16
&END QM_KIND
&QM_KIND H ! H atoms in the QM region
MM_INDEX 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34
&END QM_KIND
&END QMMM
&END FORCE_EVAL
&MOTION section
It contains all the parameters for the MD run (or motion of nuclei).
&MOTION ! Parameter for the motion of the nuclei
&MD ! set of parameters needed perform an MD run
ENSEMBLE NPT_I ! Ensemble/integrator that you want to use for MD
TIMESTEP [fs] 0.5 ! Time step
STEPS 200 ! Number of MD steps to perform
TEMPERATURE 298 ! Temperature in K
&BAROSTAT ! Parameters of barostat.
TIMECON [fs] 100
PRESSURE [bar] 1.0
&END BAROSTAT
&THERMOSTAT ! Parameters of Thermostat.
REGION GLOBAL ! region each thermostat is attached to.
TYPE CSVR ! canonical sampling through velocity rescaling
&CSVR
TIMECON [fs] 10.
&END CSVR
&END THERMOSTAT
&END MD
&PRINT ! Printing properties during an MD run
&RESTART ! Printing of restart files
&EACH ! A restart file will be printed every 2000 md steps
MD 2000
&END
&END
&TRAJECTORY ! Controls the output of the trajectory
FORMAT DCD ! Format of the output trajectory is DCD
&EACH ! New trajectory frame will be printed each 100 md steps
MD 100
&END
&END
&RESTART_HISTORY ! Controls printing of unique restart files during the run keeping all of them.
&EACH ! A new restart file will be printed every 5000 md steps
MD 5000
&END
&END
&CELL ! Controls the output of cell dimensions
&EACH ! Cell dimensions will be printed each 100 md steps
MD 100
&END
&END
&END PRINT
&END MOTION