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Acetone: Coordinate File File: ACET acetone.rst 10 NATOM,TIME (I5,5E15.7) O 3.5369136 1.4228577 -0.0000019 C 3.9514241 0.7083417 -0.8923606 C 3.1046075 -0.4091605 -1.4792938 H 2.9613371 -0.2564607 -2.5551062 H 3.6104655 -1.3742500 -1.3612860 H 2.1359290 -0.4389819 -0.9804223 C 5.3408964 0.8879357 -1.4792794 H 5.2805369 1.0887746 -2.5550287 H 5.8482060 1.7136823 -0.9804012 H 5.9284698 -0.0297019 -1.3613192 X,Y,Z : coordinates : FORMAT(6F12.7) (X(i), Y(i), Z(i), i = 1,NATOM) IF dynamics FORMAT(6F12.7) (VX(i), VY(i), VZ(i), i = 1,NATOM) VX,VY,VZ : velocities (units: Angstroms per 1/20.455 ps) IF constant pressure (in 4.1, also constant volume) FORMAT(6F12.7) BOX(1), BOX(2), BOX(3) BOX : size of the periodic box • the informa4on from the topology and the coordinate files need to be combined to describe the system.
Acetone in Water: Water Box – Automa4c genera4on of a periodic solvent rectangular box solvateBox solute solvent distance [closeness] solvateBox ACET TIP3PBOX 14 • solute UNIT (here: ACET) is modified by addi4on of solvent residues • distance: closest distance between any atom of the solute and the edge of the periodic box. • closeness: criterion for rejec4on of overlapping solute/solvent residues [factor mul4plies the sum of van-‐der-‐Waals radii of solute and solvent atoms (default = 1)] – Export the topology and coordinate files for the solvated system saveAmberParm ACET acetone_solv.top acetone_solv.rst
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 39 and 40: Force field: Bonded terms (not used
Page 41 and 42: Acetone in Water: Electrostatic Int
Page 45 and 46: Running Gaussian 1. Set the envir
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: Acetone: Topology File %VERSION VER
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
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