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QM/MM Output: Simulated Annealing • annealing.out (con4nued) – averages and root mean squared devia4ons • useful to detect unwanted energy dri‚s or too large fluctua4ons **************************************************************** * AVERAGED QUANTITIES * **************************************************************** MEAN VALUE +/- RMS DEVIATION [-^2]**(1/2) ELECTRON KINETIC ENERGY 0.000867 0.300539E-03 IONIC TEMPERATURE 37.2640 52.8318 DENSITY FUNCTIONAL ENERGY -56.788301 0.907159 CLASSICAL ENERGY -56.369667 1.48329 CONSERVED ENERGY -56.368800 1.48357 NOSE ENERGY ELECTRONS 0.000000 0.00000 NOSE ENERGY IONS 0.000000 0.00000 CONSTRAINTS ENERGY 0.000000 0.00000 RESTRAINTS ENERGY 0.000000 0.00000 ION DISPLACEMENT 0.306287 0.932230E-01 CPU TIME 1.5641
QM/MM Output: Simulated Annealing • annealing.out (con4nued) – final energies **************************************************************** ELECTRONIC GRADIENT: MAX. COMPONENT = 1.11491E-03 NORM = 1.23088E-04 TOTAL INTEGRATED ELECTRONIC DENSITY IN G-SPACE = 24.000000 IN R-SPACE = 24.000000 (K+E1+L+N+X+Q+M) TOTAL ENERGY = -57.65483705 A.U. (K+E1+L+N+X) TOTAL QM ENERGY = -36.47961427 A.U. (Q) TOTAL QM/MM ENERGY = 0.00000000 A.U. (M) TOTAL MM ENERGY = -21.15838639 A.U. DIFFERENCE = -0.01683640 A.U. (K) KINETIC ENERGY = 27.71417532 A.U. (E1=A-S+R) ELECTROSTATIC ENERGY = -27.62253859 A.U. (S) ESELF = 29.92067103 A.U. (R) ESR = 1.68735525 A.U. (L) LOCAL PSEUDOPOTENTIAL ENERGY = -29.40960654 A.U. (N) N-L PSEUDOPOTENTIAL ENERGY = 3.57453859 A.U. (X) EXCHANGE-CORRELATION ENERGY = -10.73618306 A.U. GRADIENT CORRECTION ENERGY = -0.58308674 A.U. ****************************************************************
Page 1 and 2:
From Molecular to Con/nuum Phys
Page 3 and 4:
Car-Parinello / Molecular Mechanics
Page 5 and 6:
Potential Energy Surfaces • Geome
Page 7 and 8:
Molecular Dipole Moments • Molecu
Page 9 and 10:
Quantum Mechanical Dipole Moments
Page 11 and 12:
Molecular Dipole Moments Alignment
Page 13 and 14:
Dipole Moment Of Acetone • Proced
Page 15 and 16:
Internal Coordinates Bond lengths
Page 17 and 18:
CPMD Input • General - Sec4ons:
Page 19 and 20:
CPMD Input • &SYSTEM … &END
Page 21 and 22:
Choosing the Plane Wave Cutoff •
Page 23 and 24:
CPMD Input • &ATOMS … &END (
Page 25 and 26:
CPMD Output • Header - Date whe
Page 27 and 28:
CPMD Output • Atoms: coordinates
Page 29 and 30:
CPMD Output • Distribu4on among
Page 31 and 32:
CPMD Output • Ini4al guess for
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CPMD Output • Geometry op4miza4o
Page 35 and 36:
Page 37 and 38:
Page 39 and 40:
Force field: Bonded terms (not used
Page 41 and 42:
Acetone in Water: Electrostatic Int
Page 43 and 44:
Page 45 and 46:
Running Gaussian 1. Set the envir
Page 47 and 48:
Page 49 and 50:
Antechamber - automates the proce
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Antechamber - automates the proce
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Antechamber - rapid genera4on of
Page 55 and 56:
Acetone: Pre-Equilibration • Clas
Page 57 and 58:
Acetone: Topology File %VERSION VER
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Acetone in Water: Water Box - Autom
Page 61 and 62:
Water Models - Water models diffe
Page 63 and 64:
Water Models http://www.lsbu.ac.uk/
Page 65 and 66: Sander: Pre-Equilibration • 1. C
Page 67 and 68: Sander: Usage
Page 69 and 70: Sander: 1. Restrained Minimization
Page 71 and 72: Sander: 2. Unrestrained Minimizatio
Page 73 and 74: Sander: 3. MD at 300 K (NVT ensembl
Page 75 and 76: Vibrational Motions • High-‐f
Page 77 and 78: Statistical Thermodynamics • Cano
Page 79 and 80: Sander: 3. MD at 300 K (Heating)
Page 81 and 82: Sander: 4. MD at 300 K / 1 atm (NPT
Page 83 and 84: Analysis and Processing: Reimaging
Page 85 and 86: Ab initio MD • Born-‐Oppenhei
Page 87 and 88: Ab initio MD: CPMD • Adiaba4c se
Page 89 and 90: Ab initio MD: CPMD • How to con
Page 91 and 92: QM/MM: Production • Controlling
Page 93 and 94: QM/MM • Combina4on of accuracy
Page 95 and 96: QM/MM: Electrostatic interaction
Page 97 and 98: QM/MM: CPMD/GROMOS • Hamiltonian
Page 99 and 100: QM/MM: CPMD/GROMOS • Long-‐ra
Page 101 and 102: QM/MM: CPMD/GROMOS • Forces •
Page 103 and 104: QM/MM Input: Classical Input File T
Page 105 and 106: QM/MM Input: Classical Topology Fil
Page 107 and 108: QM/MM Input: Classical Topology Fil
Page 109 and 110: QM/MM Input: QM Part - CPMD Input &
Page 111 and 112: QM/MM Input: QM Part - CPMD Input &
Page 113 and 114: QM/MM Output: Simulated Annealing
Page 115: Car-Parrinello Lagrangian L = T −
Page 119 and 120: QM/MM Output: Simulated Annealing 9
Page 121 and 122: QM/MM: Test - Result: temperature
Page 123 and 124: QM/MM: Heating - Hea4ng of the s
Page 125 and 126: QM/MM: Production • QM/MM-‐CP
Page 127 and 128: QM/MM: Dipole Moment Calculation -
Page 129 and 130: QM/MM: Dipole Moment Calculation
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