C***********************************************************************C C HYBRID ZINDO / MOLECULAR MECHANICS (ZINDO/MM) PROGRAM C C PROGRAM MANUAL C C C C C C C C C C WRITTEN BY : GREG PEARL* C C QUANTUM THEORY PROJECT C C PEARL@QTP.UFL.EDU C C C C ANDERS BROO C C CHALMERS UNIVERSITY OF TECHNOLOGY C C BROO@PHC.CHALMERS.SE C C C C DATE : 06-27-1996 C C C C***********************************************************************C I. <<<<< INTRODUCTION II. <<<<< COMBINED QM/MM SIMULATION III. <<<<< KEYWORDS IV. <<<<< EXAMPLE INPUTS X. <<<<< REFERENCES ------------------------------------------------------------------------------- =============================================================================== ------------------------------------------------------------------------------- I. INTRODUCTION This is a Hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) which is based upon the ZINDO semi empirical qmantum mechanics program in conjunction with any All atom force field. The force fields currently being used are SPC, AMBER, CHARMm. The Lennard-Jones interactions between the Quantum mechanics and molecular mechanics region uses these same parameters with a constant scaling factor for both the terms. This QM/MM code has been written inside of the ZINDO code, therefore most of the features of ZINDO can also be utilized in this code, such as solvation models, and all the SCFTYP's work for the mixed mode calculations. This code incorperates a geometry optimizer, molecular dynamics, and Monte Carlo methods for searching phase space. All of the methods will work for a total quantum mechanics system, total classical system, or a hybrid QM/MM system. The Geometry optimizers has several different methods for determing the minimum energy which include steepest descent (SD), Broyden-Fletcher- Goldfarb-Shanno Hessian update method (BFGS), DFP, Green, and MURSAR. The molecular dynamics uses an NVT (NVE) ensemble for calculation of the thermodynamic properties. The equations of motion which are used for calculating the next step are: r(t + dt) = r(t) + dtv(t) + {4a(t) - a(t - dt)}dt**2 / 6 v(t + dt) = r(t + dt) / dt - r(t) / dt + {2a(t + dt) + a(t)}dt / 6 the stability of the integration is determined by the R.M.S. fluctuation in the energy. The temperature is scale using the Berendsen heat bath scaling. The Monte Carloo simulations follow the procedure outlined by Metropolis in 1949. The NVT (NVE) ensemble is also choosen for calculating the thermodynamic properties of the system by default. The NPT and other ensembles should be implemented in the near future. The random number generator chosen for the Monte Carlo simulations has a period of approximately 2E9. ------------------------------------------------------------------------------- =============================================================================== ------------------------------------------------------------------------------- IV. QM/MM The QM/MM subroutines use the ZINDO Semi-Empirical Hamilitonian with an electronic QM/MM Hamilitonian added to it. The Classical Mechanics energies are calculated and then added to the Quantum Mechanics Energy after it has been normalized. For more details see Broo, Pearl, and Zerner 'insert' reference here. ------------------------------------------------------------------------------- =============================================================================== ------------------------------------------------------------------------------- V. KEYWORDS The following is a list of all the Keywords used by the QMMM subroutine. >>>>> $CONTRL INPUT BLOCK The $CONTRL input block is the same as a normal ZINDO except that there are two new KEYWORDS and one new RUNTYP. RUNTYP = QMMM Indicates that this is a QM/MM run QMMMTYP = Type of QM/MM calculation QMMMBND = Type of Boundary conditions for simulation QMMMTYP can be any of the following methods: G-SD Geometry Optimization using steepest descent G-BFGS Geometry Optimization using BFGS Hesian update method G-DFP Geometry Optimization using DFP Hessian update method G-GREEN Geometry Optimization using Green's Hessian update method G-MUR Geometry Optimization using MURSAR Hessian update method MD Molecular Dynamics using the NVE ensemble MC Monte Carlo using the NVE ensemble QMMMBND can be any of the following: NONE No boundary coditions; default choice if KEYWORD not given PBC Cubic Periodic Boundary Conditions MPBC Minimal Cubic Periodic Boundary Conditions =============================================================================== EXAMPLE INPUT: $CNTRL SCFTYP = ROHF RUNTYP = QMMM QMMMTYP = G-SD ENTTYP = COORD UNITS = ANGS INTTYP = 0 IAPX = 3 NAT = 4 PTCG = 3 IPRINT = -1 NEL = 12 MULT = 1 ITMAX = 200 SCFTOL = 0.1D-8 IDD2 = 0 NOP = 2 NDT = 1 ONAME = qmmm-rohf QMMMBND = NONE FOP(1) = 10.000000 2.000000 INTFA(1) = 1.0 1.0 1.0 1.0 1.0 1.0 $END =============================================================================== >>>>> $DATAIN INPUT BLOCK This input block is the same as the standard input block used for the ZINDO program. See ccc.hlp or manuals/user.manual =============================================================================== EXAMPLE INPUT: $DATAIN -1.8200 0.6400 0.0000 8 END -0.7700 0.0300 0.0000 6 END 0.1700 0.5700 0.0000 1 END -0.7700 -1.0500 0.0000 1 END $END =============================================================================== >>>>> $PTCHGI INPUT BLOCK The $PTCHGI input block is used to read in the Classical atoms. VARIABLES READ IN : COCL is the X,Y,Z coordinates for the Classical Atoms. REAL MCL is the Atomic Number (O = 8, N = 7, C = 6, ect...) INTEGER QCL is the net charge on an atom REAL NCL is the Atom Type for the Classical Force Fields =====> You must assign the Classical atoms a charge, usually the 6-31G =====> or higher level Muliken charges are used. This is critical for =====> the QM/MM method to work, since the coulombic interactions are =====> approximately 1/2 the interaction forces between the QM and CM =====> partitions. See papers refering to the original paramiterization =====> of the force field being used. C****************************************************************************** C C TABLE OF ACCEPTED NCL VALUES : C C # TYPE OF ATOM SYMBOL COMMENTS C ---------------------------------------------------------------------- C 1 == CARBONYL OXYGEN (O) C 2 == HYDROXYL OXYGEN (OH1) C 3 == CARBOXYL OXYGEN (OM) C 4 == NITOGEN (N) C 5 == 1/3 CHARGED NITROGEN (NC2) C 6 == NH3 TERMINAL GROUP (NC3) C 7 == ALIPHATIC CH CARBON (CH1) C 8 == ALIPHATIC CH2 CARBON (CH2) C 9 == ALIPHATIC CH3 CARBON (CH3) C 10 == BARE CARBON (C) C 11 == AROMATIC CARBON (CR1) C 12 == SULFUR (S) C 13 == HYDROGEN (H) C 14 == NONPOLAR HYDROGEN (HC) C 15 == AROMATIC NITROGEN (NR) C 16 == DOUBLE BONDED NITROGEN (NH1) C 17 == CALCIUM ION (CA) C 18 == OXYGEN IN WATER (OWTR) C 19 == HYDROGEN IN WATER (HWTR) C 20 == SODIUM ION (NA) C 21 == RUTHENIUM (RU) ADDED BY ANDERS BROO 07-17-91 C C****************************************************************************** In order to add new atom type you must modify the force field file INPUT FORM: $PTCHGI TITLE "Screening Constant" , "Bulk Dielectric" X,Y,Z,MCL,QCL,NCL ... ... $END =============================================================================== EXAMPLE INPUT: $PTCHGI CLASSICAL WATER MOLECULE 0.00000 0.00000 -4.4500 -0.6000 0.0000 1 0.41 19 -4.4500 0.3600 0.0000 8 -0.82 18 -3.5500 0.6800 0.0000 1 0.41 19 $END =============================================================================== >>>>> $CLASIC Input Block This input block is the main input block for the classical mechanics partition of the program. THIS BLOCK IS REQUIRED FOR ALL TYPES OF QM/MM SIMULATIONS VARIABLES READ IN : LINE VARIABLE DESCRIPTION ------------------------------------------------------------------------------- 1 RESTART -- THIS DETERMINES IF THIS IS A CONTINUING A SIMULATION OR A NEW SIMULATION. NEW,OLD ARE THE ONLY ACCEPTABLE RESPONCES 2 NATOM -- THE NUMBER OF ATOMS IN THE SIMULATION 2 NMOL -- THE NUMBER OF MOLECULES IN THE SIMULATION 2 NMQM -- THE NUMBER OF MOLECULES WHICH ARE QUANTUM 2 NMCL -- THE NUMBER OF MOLECULES WHICH ARE CLASSICAL 3 ATOM# -- THE ATOM NUMBER FOR EACH ATOM. 3 MOL# -- SPECIFIES WHICH MOLECULE THE ATOM IS IN. 3 QM/MM -- THIS SPECIFIES HOW THE ATOM IS TO BE MODELED 1 = QUANTUM MECHANICS (ZINDO) 2 = CLASSICAL MECHANICS (FORCE FIELD) 3 POT -- THIS ALLOWS YOU TO ADD FORCE FIELD PARAMETERS WITHOUT HAVING TO RECOMPILE THE CODE. 0 = READ PARAMETERS FROM THE FORCE FIELD FILE 1 = READ PARAMETERS FROM INPUT FILE 3 BOND -- SPECIFIES WHICH ATOM THAT THIS ATOM IS BONDED TO (CLASSICAL MECHANICS ONLY) ------------------------------------------------------------------------------- INPUT FORM: $CLASIC RESTART NATOM,NMOL,IBND ATOM#,MOL#,QM/MM,POT,BOND,BOND,BOND,BOND,BOND ... ... ... $END =============================================================================== EXAMPLE INPUT: $CLASIC NEW 6 2 0 0 1 1 1 0 19 0 0 0 0 0 2 1 1 0 18 0 0 0 0 0 3 1 1 0 19 0 0 0 0 0 4 2 2 0 5 0 0 0 0 0 5 2 2 0 6 0 0 0 0 0 6 2 2 0 0 0 0 0 0 0 $END =============================================================================== >>>>> $QCMDIN Input Block The $QCMDIN Input Block is only used if you specified QMMMTYP = MD. This input block contains the information which is specifically needed to run a dynamics simulation. VARIABLES READ IN : LINE VARIABLE DESCRIPTION ------------------------------------------------------------------------------- 1 MSTEP -- THIS IS THE NUMBER OF DYNAMIC STEPS TO RUN 1 OUTPUT -- FREQUENCY TO PRINT OUT MOVIE.XYZ FILE 2 STEP SIZE -- SIZE OF EACH STEP IN SECONDS 2 TEMP -- THE DESIRED SIMULATION TEMPERATURE 2 TAUTEMP -- FRICTION COEFF. FOR HEAT BATH; FOUND THAT 1X10^-11 -- 1X10^-16 ARE OK VALUES 2 NONBND -- NONBONDED CUTOFF RANGE, 20 A IS VERY GOOD; 12 A IS ACCEPTABLE 3 POTLIB -- NAME OF THE FILE CONTAINING THE FORCE FIELD POTENTIALS 4 BOXA -- X BOX LENGTH, PBC 4 BOXB -- Y BOX LENGTH, PBC 4 BOXC -- Z BOX LENGTH, PBC ------------------------------------------------------------------------------- INPUT FORM : $QCMDIN MSTEP,OUTPUT STEP SIZE,TEMP,TAUTEMP,NONBND POTLIB BOXA,BOXB,BOXC $END =============================================================================== EXAMPLE INPUT: $QCMDIN 500 10 01.E-15 200.0 0.7E-12 20.0 /afs/root/usr/lic/src/zindo/source/qcmd.lib 20.0 20.0 20.0 $END =============================================================================== >>>>> QCMCIN Input Block is only required if the QMMMTYP indicates that this is a Monte Carlo Calculation. LINE VARIABLE DESCRIPTION ------------------------------------------------------------------------------- 1 TEMP -- THE DESIRED SIMULATION TEMPERATURE 1 NONBND -- NONBONDED CUTOFF RANGE 4 BOXA -- X LENGTH FOR PBC BOX 4 BOXB -- Y LENGTH FOR PBC BOX 4 BOXC -- Z LENGTH FOR PBC BOX 2 ICONF -- THE NUMBER OF DIFFERENT CONFIGURATIONS YOU WANT. MAXIMUM NUMBER (10,000) 3 POTLIB -- NAME OF THE FILE CONTAINING THE FORCE FIELD POTENTIALS ------------------------------------------------------------------------------- INPUT FORM: $QCMCIN TEMP,NONBND ICONF POTLIB BOXA,BOXB,BOXC $END =============================================================================== EXAMPLE INPUT: $QCMCIN 0.10 20.0 200 /afs/root/usr/lic/src/zindo/source/qcmd.lib $END =============================================================================== >>>>> QCGIN Input Block is only needed if the QMMMTYP indicates that the calculation is to be a geometry optimization. LINE VARIABLE DESCRIPTION ------------------------------------------------------------------------------- 1 STEP -- SIZE OF THE SD STEP IN ANGSTROMS, NEEDED FOR ALL TYPES OF GEOMETRY OPTIMIZATIONS. SINCE THEY TAKE AN INITIAL SD STEP. 1 ETOL -- DIFFERENCE IN ENERGY TOLERENCE (KJ/MOL) 1 GTOL -- THE NORMAL GRADIENT SIZE TOLERENCE, USUALLY 0.1 * ETOL 1 NONBND -- NONBONDED CUTOFF RANGE 2 MSTEP -- MAXIMUM NUMBER OF STEPS TO TAKE, SHOULD NOT BE MORE THAN 5 * # ATOMS. 3 POTLIB -- NAME OF THE FILE CONTAINING THE FORCE POTENTIALS ------------------------------------------------------------------------------- INPUT FORM: $QCGIN STEP,ETOL,GTOL,CUTOFF,NONBND MSTEP POTLIB $END =============================================================================== EXAMPLE INPUT: $QCGIN 0.1 0.001 0.0001 200 /afs/root/usr/lic/src/zindo/source/qcmd.lib $END =============================================================================== ------------------------------------------------------------------------------- =============================================================================== ------------------------------------------------------------------------------- VI. EXAMPLE INPUTS =============================================================================== $TITLEI QM/MM TEST CASE #1 2 CLASSICAL MECHANICS WATER MOLECULES TESTS: MOLECULAR DYNAMICS; CLASSICAL FORCES $END $CONTRL IPRINT = -1 SCFTYP = RHF RUNTYP = QMMM QMMMTYP = MD ENTTYP = COORD UNITS = ANGS CHARGE = 0 ONAME = mm1 NAT = 0 PTCG = 6 MULT = 1 ITMAX = 250 SCFTOL = 0.1D-8 IAPX = 3 INTTYP = 0 INTFA(1) = 1.0 1.000 1.0 1.0 1.0 1.0 $END $DATAIN $END $QCMDIN 500 100 0 0.5E-15 20.0 0.07E-12 20.0 /ufl/qtp/mcz/progs/zindo/ForceFields/qcmd.lib $END $QCGIN 0.002 1.0D-6 1.0D-5 10. 100 /ufl/qtp/mcz/progs/zindo/ForceFields/qcmd.lib $END $PTCHGI Water Dimer Test Case CL-CL 0.0 0.0 1.74916433 0.75016382 0.00000000 1 0.41 19 1.33718044 -0.16543844 0.00000000 8 -0.82 18 2.07524716 -0.84082824 0.00000000 1 0.41 19 -0.42532050 0.00000000 0.08384480 1 0.41 19 -1.43532546 0.00000000 0.20931161 8 -0.82 18 -1.85989940 0.00000000 -0.69193071 1 0.41 19 $END $CLASIC NEW 6 2 0 2 1 1 2 0 2 0 0 0 0 2 1 2 0 3 0 0 0 0 3 1 2 0 0 0 0 0 0 4 2 2 0 5 0 0 0 0 5 2 2 0 6 0 0 0 0 6 2 2 0 0 0 0 0 0 $END =============================================================================== $TITLEI QM/MM TEST CASE #4 2 WATERS WITH 1)QUANTUM MECHANICS 1) CLASSICAL MECHANICS TESTS: GEOMETRY OPTIMIZER STEEPEST DESCENT; QUANTUM FORCES; SCFTYP = ROHF; QM/MM INTERACTION FORCES; $END $CONTRL IPRINT = -1 SCFTYP = RHF RUNTYP = QMMM QMMMTYP = G-SD ENTTYP = COORD UNITS = ANGS CHARGE = 0 ONAME = mm4 NAT = 3 PTCG = 3 MULT = 3 ITMAX = 150 SCFTOL = 0.00001 IAPX = 3 INTTYP = 0 NOP 2 NDT 1 FOP(1) = 10.000000 2.000000 INTFA(1) = 1.0 1.000 1.0 1.0 1.0 1.0 $END $DATAIN 1.74916433 0.75016382 0.00000000 1 END 1.33718044 -0.16543844 0.00000000 8 END 2.07524716 -0.84082824 0.00000000 1 END $END $PTCHGI Water Dimer Test Case QM-CL 0.0 0.0 -0.425320 0.000000 0.083844 1 0.410000 19 -1.435325 0.000000 0.209311 8 -0.820000 18 -1.859899 0.000000 -0.691930 1 0.410000 19 $END $QCGIN 0.02 0.01 0.001 30. 20 /ufl/qtp/mcz/progs/zindo/ForceFields/qcmd.lib $END $QCMDIN 500 10 0 0.1E-15 0.1 0.7E-12 20.0 /ufl/qtp/mcz/progs/zindo/ForceFields/qcmd.lib 15.0 15.0 15.0 $END $CLASIC NEW 6 2 1 1 1 1 1 0 19 0 0 0 0 0 2 1 1 0 18 0 0 0 0 0 3 1 1 0 19 0 0 0 0 0 4 2 2 0 5 0 0 0 0 0 5 2 2 0 6 0 0 0 0 0 6 2 2 0 0 0 0 0 0 0 $END $BETAIN ! s s s s p p p p d d f f ! atomic numbers - there must be 12 6 7 8 1 6 7 8 1 0 0 0 0 ! THe 12 beta values corresponing to the above atomic numbers (eV) ! -17.0 -26.0 -35.0 -11.80 -17.0 -26.0 -35.0 -1.00 -0.00 -0.00 -0.00 -0.00 -26.0 -26.0 -35.0 -12.60 -16.32 -32.94 -40.0 -1.00 -0.00 -0.00 -0.00 -0.00 $END =============================================================================== $TITLEI QM/MM TEST CASE #5 2 WATERS WITH 1)QUANTUM MECHANICS 1) CLASSICAL MECHANICS TESTS: MONTE CARLO; QUANTUM FORCES; SCFTYP = RHF; QM/MM INTERACTION; SCRF INTERACTION; BETA CHANGING $END $CONTRL IPRINT = -1 SCFTYP = RHF RUNTYP = QMMM QMMMTYP = MC ENTTYP = COORD UNITS = ANGS CHARGE = 0 ONAME = mm5 NAT = 3 PTCG = 3 MULT = 1 ITMAX = 150 SCFTOL = 0.00001 IAPX = 3 INTTYP = 0 ISCRF 6 INTFA(1) = 1.0 1.000 1.0 1.0 1.0 1.0 $END $DATAIN 1.74916433 0.75016382 0.00000000 1 END 1.33718044 -0.16543844 0.00000000 8 END 2.07524716 -0.84082824 0.00000000 1 END $END $PTCHGI Water Dimer Test Case QM-CL 0.0 0.0 -0.42532050 0.00000000 0.08384480 1 0.41 19 -1.43532546 0.00000000 0.20931161 8 -0.82 18 -1.85989940 0.00000000 -0.69193071 1 0.41 19 $END $QCMDIN 15 5 0 0.5E-15 20.0 0.07E-12 20.0 /ufl/qtp/mcz/progs/zindo/ForceFields/qcmd.lib $END $QCMCIN 1000.0 20.0 5 /ufl/qtp/mcz/progs/zindo/ForceFields/qcmd.lib $END $CLASIC NEW 6 2 1 1 1 1 1 0 19 0 0 0 0 0 2 1 1 0 18 0 0 0 0 0 3 1 1 0 19 0 0 0 0 0 4 2 2 0 5 0 0 0 0 0 5 2 2 0 6 0 0 0 0 0 6 2 2 0 0 0 0 0 0 0 $END $SCRFIN ! ***** Self consistent reaction field information ***** 6 1 0 0.000000 78.500000 1.332870 $END $BETAIN ! s s s s p p p p d d f f ! atomic numbers - there must be 12 6 7 8 1 6 7 8 1 0 0 0 0 ! THe 12 beta values corresponing to the above atomic numbers (eV) ! -17.0 -26.0 -35.0 -11.80 -17.0 -26.0 -35.0 -1.00 -0.00 -0.00 -0.00 -0.00 -26.0 -26.0 -35.0 -12.60 -16.32 -32.94 -40.0 -1.00 -0.00 -0.00 -0.00 -0.00 $END =============================================================================== ------------------------------------------------------------------------------- =============================================================================== ------------------------------------------------------------------------------- X. 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Zerner Quantum Theory Project, Department of Chemistry, University of Florida, 23) "Numerical Recipes in FORTRAN" 2nd Ed. Cambridge University Press 1992