- 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: Quantum Mechanical Dipole Moments
- 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
- Page 33 and 34: CPMD Output • Geometry op4miza4o
- Page 35 and 36: CPMD Output • Geometry op4miza4o
- Page 37 and 38: CPMD Output • Geometry op4miza4o
- Page 39 and 40: Force field: Bonded terms (not used
- Page 41 and 42: Acetone in Water: Electrostatic Int
- Page 43 and 44: Acetone in Water: Electrostatic Int
- Page 45 and 46: Running Gaussian 1. Set the envir
- Page 47 and 48: Acetone in Water: Electrostatic Int
- Page 49 and 50: Antechamber - automates the proce
- Page 51 and 52: Antechamber - automates the proce
- Page 53 and 54: Antechamber - rapid genera4on of
- Page 55 and 56: Acetone: Pre-Equilibration • Clas
- Page 57 and 58: Acetone: Topology File %VERSION VER
- Page 59 and 60: 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 and 116:
Car-Parrinello Lagrangian L = T −
- Page 117 and 118:
QM/MM Output: Simulated Annealing
- 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