#Generated by Multiwfn
&GLOBAL
PROJECT Protein_solv_Monitor_PBE
PRINT_LEVEL LOW
RUN_TYPE MD
&END GLOBAL
&FORCE_EVAL
METHOD QMMM
STRESS_TENSOR ANALYTICAL
&DFT
BASIS_SET_FILE_NAME EMSL_BASIS_SETS
POTENTIAL_FILE_NAME POTENTIAL
WFN_RESTART_FILE_NAME 5NMY_solv_monitor_pbe-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
EXTRAPOLATION PS #Extrapolation for wavefunction during e.g. MD. ASPC is default, PS also be used
EXTRAPOLATION_ORDER 2 #Order for PS or ASPC extrapolation. 3 is default
METHOD GAPW
&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
&END XC_FUNCTIONAL
&VDW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
PARAMETER_FILE_NAME dftd3.dat
TYPE DFTD3
REFERENCE_FUNCTIONAL PBE
&END PAIR_POTENTIAL
&END VDW_POTENTIAL
&END XC
&MGRID
CUTOFF 400
REL_CUTOFF 55
COMMENSURATE
&END MGRID
&SCF
MAX_SCF 128
EPS_SCF 3.0E-05 #Convergence threshold of density matrix during SCF
SCF_GUESS RESTART #Use wavefunction from WFN_RESTART_FILE_NAME file as initial guess
&DIAGONALIZATION
ALGORITHM STANDARD #Algorithm for diagonalization. DAVIDSON is faster for large systems
&END DIAGONALIZATION
&MIXING #How to mix old and new density matrices
METHOD BROYDEN_MIXING #PULAY_MIXING is also a good alternative
ALPHA 0.4 #Default. Mixing 40% of new density matrix with the old one
NBROYDEN 32 #Default is 4. Number of previous steps stored for the actual mixing scheme
&END MIXING
&OUTER_SCF
MAX_SCF 64 #Maximum number of steps of outer SCF
EPS_SCF 1.0E-05 #Convergence threshold of outer SCF
&END OUTER_SCF
&SMEAR
METHOD FERMI_DIRAC
ELECTRONIC_TEMPERATURE 300 #Electronic temperature of Fermi-Dirac smearing in K
&END SMEAR
ADDED_MOS 100 #Number of virtual MOs to be solved
&PRINT
&RESTART #Use "&RESTART OFF" can prevent generating wfn file
BACKUP_COPIES 0 #Maximum number of backup copies of wfn file
&END RESTART
&END PRINT
&END SCF
&PRINT
&MO_MOLDEN
NDIGITS 8
GTO_KIND SPHERICAL
&END MO_MOLDEN
&MULLIKEN
FILENAME=mulliken
COMMON_ITERATION_LEVELS 10
&EACH
MD 1
&END EACH
&END MULLIKEN
&PDOS
NLUMO -1
&END PDOS
&END PRINT
&END DFT
&MM
&FORCEFIELD
PARMTYPE AMBER
PARM_FILE_NAME 5NMY_solv_LJ_mod.prmtop
&SPLINE
EMAX_SPLINE 1.0E3
RCUT_NB [angstrom] 10
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA .40
GMAX 80
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
A 68.76848667 0.00000000 0.00000000
B 0.00000000 66.604543937 0.00000000
C 0.00000000 0.00000000 86.978811596
PERIODIC XYZ #Direction of applied PBC (geometry aspect)
&END CELL
&TOPOLOGY
CONN_FILE_FORMAT AMBER
CONN_FILE_NAME 5NMY_solv_LJ_mod.prmtop
&END TOPOLOGY
# &VELOCITY #You can set initial atomic velocities in this section
# &END VELOCITY
&KIND N
ELEMENT N
BASIS_SET Ahlrichs-def2-SVP
POTENTIAL ALL
&END KIND
&KIND H
ELEMENT H
BASIS_SET Ahlrichs-def2-SVP
POTENTIAL ALL
&END KIND
&KIND HX
ELEMENT H
BASIS_SET Ahlrichs-def2-SVP
POTENTIAL ALL
&END KIND
&KIND C
ELEMENT C
BASIS_SET Ahlrichs-def2-SVP
POTENTIAL ALL
&END KIND
&KIND O
ELEMENT O
BASIS_SET Ahlrichs-def2-SVP
POTENTIAL ALL
&END KIND
&KIND He
ELEMENT He
BASIS_SET Ahlrichs-def2-SVP
POTENTIAL ALL
&END KIND
&KIND S
ELEMENT S
BASIS_SET Ahlrichs-def2-SVP
POTENTIAL ALL
&END KIND
&KIND La
ELEMENT La
BASIS_SET Ahlrichs-def2-SVP
POTENTIAL ALL
&END KIND
&KIND M1
ELEMENT La
BASIS_SET Ahlrichs-def2-SVP
POTENTIAL ALL
&END KIND
&KIND Cl-
ELEMENT Cl
BASIS_SET Ahlrichs-def2-SVP
POTENTIAL ALL
&END KIND
&COLVAR
&DISTANCE
ATOMS 3739 3740
&END DISTANCE
&END COLVAR
&COLVAR
&DISTANCE
ATOMS 3733 3734
&END DISTANCE
&END COLVAR
&COLVAR
&DISTANCE
ATOMS 3725 3727
&END DISTANCE
&END COLVAR
&END SUBSYS
&QMMM
ECOUPL GAUSS
CENTER EVERY_STEP
NOCOMPATIBILITY
USE_GEEP_LIB 8
PARALLEL_SCHEME GRID
&CELL
ABC 40 40 40
ALPHA_BETA_GAMMA 90 90 90
&END CELL
&LINK
ALPHA 1.50
LINK_TYPE IMOMM
MM_INDEX 444
QM_INDEX 446
&END LINK
&LINK
ALPHA 1.50
LINK_TYPE IMOMM
MM_INDEX 463
QM_INDEX 461
&END LINK
&MOTION
&MD
ENSEMBLE NVT
STEPS 10000
TIMESTEP [fs] 0.5 #fs. Decrease it properly for high temperature simulation
TEMPERATURE 310.15 #Initial and maintained temperature (K)
&THERMOSTAT
TYPE CSVR
&CSVR
TIMECON 200 #Time constant in fs. Smaller/larger results in stronger/weaker temperature coupling
&END CSVR
&END THERMOSTAT
&END MD
&FREE_ENERGY
METHOD METADYN
&METADYN
DO_HILLS .FALSE.
NT_HILLS 100
WW [kcalmol] 1.5
&METAVAR
WIDTH 0.5 !Also known as scale
COLVAR 1
&END METAVAR
&METAVAR
WIDTH 0.5 !Also known as scale
COLVAR 2
&END METAVAR
&METAVAR
WIDTH 0.5 !Also known as scale
COLVAR 3
&END METAVAR
&PRINT
&COLVAR
COMMON_ITERATION_LEVELS 3
&EACH
MD 10
&END EACH
&END COLVAR
&HILLS
&EACH
METADYNAMICS 1
&END EACH
COMMON_ITERATION_LEVELS 10
&END HILLS
&END
&END METADYN
&END FREE_ENERGY
&PRINT
&RESTART_HISTORY ! This section controls dumping of unique restart files during the run keeping all of them.Most useful if recovery is needed at a later point.
&EACH ! A new restart file will be printed every 10000 md steps
MD 500
&END
&END
&TRAJECTORY
&EACH
MD 100 #Output frequency of geometry
&END EACH
FORMAT xyz
&END TRAJECTORY
&VELOCITIES
&EACH
MD 100 #Output frequency of velocity
&END EACH
&END VELOCITIES
&RESTART
BACKUP_COPIES 0 #Maximum number of backing up restart file
&EACH
MD 1000 #Frequency of updating last restart file
&END EACH
&END RESTART
&END PRINT
&END MOTION