CP2K的QM/MM速度与纯QM速度会相差几十倍呢？ - 计算化学公社

&GLOBAL
PROJECT MD ! Name of the calculation
PRINT_LEVEL LOW ! Verbosity of the output
RUN_TYPE MD ! Calculation type: MD
&END GLOBAL
&FORCE_EVAL ! parameters needed to calculate energy and forces
METHOD QMMM ! Hybrid quantum classical
STRESS_TENSOR ANALYTICAL ! Compute the stress tensor analytically (if available).
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
WFN_RESTART_FILE_NAME MD-RESTART.wfn
CHARGE 0 #Net charge
MULTIPLICITY 1 #Spin multiplicity
&QS
EPS_DEFAULT 1E-10 #This is default. Set all EPS_xxx to values such that the energy will be correct up to this value
# EPS_PGF_ORB 1E-8 #If seeing "Kohn Sham matrix not 100% occupied" when using HF, MP2 or hybrid functional, uncomment this
&END QS
&POISSON
PERIODIC XYZ #Direction(s) of PBC for calculating electrostatics
PSOLVER PERIODIC #The way to solve Poisson equation
&END POISSON
&XC
&XC_FUNCTIONAL
&PBE
SCALE_X 0.75 #75% GGA exchange
SCALE_C 1.0 #100% GGA correlation
&END PBE
&END XC_FUNCTIONAL
&HF
FRACTION 0.25
&SCREENING
FRACTION 0.25
&SCREENING
EPS_SCHWARZ 1E-8 #Important to improve scaling. The larger the value, the lower the cost and lower the accuracy
SCREEN_ON_INITIAL_P T #Screening on product between maximum of density matrix elements and ERI
&END SCREENING
&INTERACTION_POTENTIAL
POTENTIAL_TYPE TRUNCATED
CUTOFF_RADIUS 6.0 #Cutoff radius for truncated 1/r potential
T_C_G_DATA t_c_g.dat
&END INTERACTION_POTENTIAL
&MEMORY
MAX_MEMORY 3000 #Memory(MB) per MPI process for calculating HF exchange
EPS_STORAGE_SCALING 0.1
&END MEMORY
&END HF
&END XC
&MGRID
COMMENSURATE
CUTOFF 300
REL_CUTOFF 40
&END MGRID
&SCF
MAX_SCF 256 #Maximum number of steps of inner SCF
EPS_SCF 1.0E-05 #Convergence threshold of density matrix of inner SCF
SCF_GUESS RESTART #Use wavefunction from WFN_RESTART_FILE_NAME file as initial guess
&OT
PRECONDITIONER FULL_SINGLE_INVERSE #Usually best but expensive for large system. Cheaper: FULL_SINGLE_INVERSE and FULL_KINETIC (default)
MINIMIZER DIIS #CG is worth to consider in difficult cases
LINESEARCH 2PNT #1D line search algorithm for CG. 2PNT is default, 3PNT is better but more costly. GOLD is best but very expensive
&END OT
&END SCF
&END DFT
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! PART2 MM
&MM ! Parameters to run a MM calculation
&FORCEFIELD ! Set up a force_field for the classical calculations
PARMTYPE AMBER ! Kind of torsion potential
! Filename that contains the parameters of the FF
PARM_FILE_NAME complex_LJ_mod.prmtop
&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
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! PART3 QMMM
&QMMM
ECOUPL GAUSS
USE_GEEP_LIB 6
MM_POTENTIAL_FILE_NAME MM_POTENTIAL
&CELL
ABC 32.2 32.2 80.0
&END CELL
!CENTER EVERY_STEP
CENTER NEVER
NOCOMPATIBILITY
&INTERPOLATOR
&INTERPOLATOR
EPS_R 1.0e-14
EPS_X 1.0e-14
MAXITER 100
&END INTERPOLATOR
&QM_KIND H
MM_INDEX 2 3 4
&END QM_KIND
&QM_KIND O
MM_INDEX 6 7 8 10 11
&END QM_KIND
&QM_KIND N
MM_INDEX 1 5 9
&END QM_KIND
&END QMMM
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! PART4 SUBSYS
&SUBSYS ! a subsystem: coordinates, topology, molecules and cell
&CELL !Set box dimensions here
ABC [angstrom] 32.2 32.2 80.0
ALPHA_BETA_GAMMA 90.0 90.0 90.0
&END CELL
&TOPOLOGY ! Topology for classical runs
CONN_FILE_FORMAT AMBER
CONN_FILE_NAME complex_LJ_mod.prmtop
COORD_FILE_FORMAT XYZ
COORD_FILE_NAME 2220.xyz
&END TOPOLOGY
&KIND O
ELEMENT O
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE
&END KIND
&KIND H
ELEMENT H
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE
&END KIND
&KIND N
ELEMENT N
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE
&END KIND
&COLVAR
&DISTANCE_FUNCTION
COEFFICIENT -1
ATOMS 1 9 1 3
&END
&END COLVAR
&END SUBSYS
&END FORCE_EVAL
&MOTION
&FREE_ENERGY
&METADYN
DO_HILLS T
!LAGRANGE F
NT_HILLS 50 !Specify the maximum MD step interval between spawning two hills
!WW 1.0e-3 !Specifies the height of the gaussian to spawn. Default 0.1
WW [kcalmol] 0.12
&METAVAR
SCALE [angstrom] 0.25
COLVAR 1
&WALL
TYPE REFLECTIVE
POSITION [angstrom] 1.35
&REFLECTIVE
DIRECTION WALL_PLUS
&END
&END
&WALL
TYPE REFLECTIVE
POSITION [angstrom] 0.80
&REFLECTIVE
DIRECTION WALL_MINUS
&END
&END
&END METAVAR
&PRINT
&COLVAR
COMMON_ITERATION_LEVELS 3
&EACH
MD 10
&END
&END
&HILLS
COMMON_ITERATION_LEVELS 3
&EACH
MD 10
&END
&END
&END
&END METADYN

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