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QM/MM Output: Simulated Annealing • annealing.out – charge compensa4on – MD energies !!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!! THE QM SYSTEM DOES NOT HAVE AN INTEGER CHARGE. A COMPENSATING CHARGE OF 0.000040 HAS BEEN DISTRIBUTED OVER THE NN ATOMS. prac4cally = 0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! NFI EKINC TEMPP EKS ECLASSIC EHAM EQM DIS TCPU 1 0.00006 297.0 -54.34715 -51.01094 -51.01088 -36.46342 0.218E-04 1.53 2 0.00056 293.9 -54.34671 -51.04477 -51.04421 -36.46309 0.863E-04 1.54 ... 1572 0.00071 3.8 -57.65444 -57.61126 -57.61055 -36.47961 0.421E+00 1.55 1573 0.00071 3.8 -57.65484 -57.61169 -57.61098 -36.47961 0.421E+00 1.60 • NFI Step number („number of finite itera4ons“ • EKINC Fic44ous kine4c energy of the electrons (should oscillate but not increase during a simula4on) • TEMPP Temperature for atoms („ions“) = „EKIONS /degrees of freedom“ • EKS Kohn-‐Sham energy (equivalent to poten4al energy in classical MD) • ECLASSIC Total energy in classical MD, but not the conserved quan4ty for CP dynamics (EKIONS + EKS) • EHAM Energy of the total CP Hamiltonian (conserved; ECLASSIC + EKINC) (depending on 4me step and electron mass this quan4ty might oscillate, but should not dri‚) • EQM Energy of QM part (contribu4ons from electrons and nuclei) • DIS Mean squared displacement of the atoms wrt ini4al coordinates (provides informa4on of diffusion)
Car-Parrinello Lagrangian L = T −V L CP = T I EKINC (T e ) 1 2 M ˙ I R 2 I + ∑ µ ˙ φ ˙ i φ i i ∑ I kinetic energy (nuclei + electrons/orbitals) EKS (V e ) − Ψ ˆ 0 H e Ψ + constraints 0 potential energy orthonormality • EKINC = T e • TEMPP = 2 / (n degrees of freedom k) with k=1.38×10 -‐23 J/K, Boltzman const. • EKS = V e (Kohn-‐Sham energy = E pot ) • ECLASSIC = E phys = T I + V e = E conserved – T e = EHAM – EKINC • EHAM = T I + T e + V e = E conserved = EHAM = ECLASSIC + EKINC (constant of mo4on)
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:
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
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: QM/MM Output: Simulated Annealing
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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