- 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
- 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: QM/MM Output: Simulated Annealing
- 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