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QM/MM Input: QM Part - CPMD Input &CPMD QMMM MOLECULAR DYNAMICS CP ISOLATED MOLECULE QUENCH BO ANNEALING IONS 0.99 TEMPERATURE 300 EMASS 600. TIMESTEP 5.0 MAXSTEP 10000 TRAJECTORY SAMPLE 0 STORE 100 RESTFILE 1 &END Calculate the ionic temperature assuming an isolated molecule of cluster (does not invoke the cluster op4on SYMMETRY 0) QUENCH: veloci4es of ions, wavefunc4ons and the cell are ini4ally set to zero. BO: converge the wave func4on in the beginning of the MD run Simulated annealing: veloci4es are mul4plied by 0.99 in every step, i.e. 1% of the kine4c energy is removed. Ini4al temperature: choosen to be the temperature from the classical equilibra4on Fic44ous electron mass: tests should verify that adia4city condi4ons are met (allows to tune, together with TIMESTEP (here ≈ 1.2 fs), the decoupling of electronic and ionic degrees of freedom). Print op4on: 0 = no trajectory is wriben. Print op4on: the RESTART file is updated every 100 steps. Number of RESTART files that are wriben in turn
QM/MM Input: QM Part - CPMD Input &SYSTEM POISSON SOLVER TUCKERMAN SYMMETRY 0 CELL 18.61 1.11 0.95 0 0 0 CUTOFF 70. CHARGE 0.0 &END &ATOMS *H_MT_BLYP.psp KLEINMAN-BYLANDER LMAX=S 6 4 5 6 8 9 10 ... &END &DFT FUNCTIONAL BLYP &END Plane wave cutoff Cell size in a.u. (1 bohr = 1 a 0 = 0.529 Å ) a b/a c/a cos cos cos Procedure to determine box size: • get QM coordinates from gromos.g96 (label CET, in nm) • sort according to increasing x value • calculate the difference between the smallest and the largest one • add 2•3.5 Å for the Poisson‘s solver requirements • convert to atomic units 6 H atoms with numbers: 4,5,6,8,9,10
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From Molecular to Con/nuum Phys
Page 3 and 4:
Car-Parinello / Molecular Mechanics
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Potential Energy Surfaces • Geome
Page 7 and 8:
Molecular Dipole Moments • Molecu
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Quantum Mechanical Dipole Moments
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Molecular Dipole Moments Alignment
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Dipole Moment Of Acetone • Proced
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Internal Coordinates Bond lengths
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CPMD Input • General - Sec4ons:
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CPMD Input • &SYSTEM … &END
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Choosing the Plane Wave Cutoff •
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CPMD Input • &ATOMS … &END (
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CPMD Output • Header - Date whe
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CPMD Output • Atoms: coordinates
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CPMD Output • Distribu4on among
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CPMD Output • Ini4al guess for
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CPMD Output • Geometry op4miza4o
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Page 37 and 38:
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Force field: Bonded terms (not used
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Acetone in Water: Electrostatic Int
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Page 45 and 46:
Running Gaussian 1. Set the envir
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Antechamber - automates the proce
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Antechamber - automates the proce
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Antechamber - rapid genera4on of
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Acetone: Pre-Equilibration • Clas
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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: 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
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