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Requests should be submitted to BIOVIA Support, either through electronic mail to [email protected], or in writing to: BIOVIA Support 5005 Wateridge Vista Drive, San Diego, CA 92121 USA Contents DMol3 1 Setting up a molecular dynamics calculation20 Introduction 1 Choosing an ensemble 21 Further Information 1 Defining the time step 21 Tasks in DMol3 2 Defining the thermostat control 21 Energy 3 Constraints during dynamics 21 Setting up the calculation 3 Setting up a transition state calculation 22 Dynamics 4 Which method to use? 22 Selecting the thermodynamic ensemble 4 Verifying a transition state 22 Defining the time step 4 Setting up a TS confirmation calculation 23 Controlling the thermostat 4 Setting up a work function calculation 23 Constraints during dynamics 4 Setting up an elastic constants calculation 24 Transition state searching 5 Parameters for the optimization 24 Transition state optimization 6 Setting up a reaction kinetics calculation 24 Transition state searching by synchronous Transition state search 25 transit methods 6 Hessian calculation 25 Verifying a transition state 7 Reaction rate calculation 25 Transition state searching via synchronous Setting up an electron transport calculation 25 transit methods 7 Requesting electronic and structural Input to a synchronous transit calculation 8 properties 26 Restarting a QST calculation 9 Setting up electron densities 27 Transition state searching via eigenvector Setting up electrostatics 27 following 9 Setting up vibrational frequencies 28 Calculation parameters 9 Setting up Raman intensities 28 Use of the Hessian 9 Setting up Fukui functions 28 Geometry optimization 9 Setting up molecular orbital analysis 29 Following a reaction path 10 Setting up a population analysis 29 Elastic constants 11 Setting up band structures 30 Reaction kinetics 11 Setting up density of states 30 Electron Transport 12 Setting up Fermi surfaces 31 Electrodes 12 Setting up COSMO Sigma profile Properties 13 calculation 31 Setting up DMol3 calculations 13 Setting up an optics calculation 31 Setting up electronic options 14 Manipulating files 32 Integration accuracy 14 Input files 32 SCF tolerance 14 Output files 33 k-points 14 Restarting a DMol3 calculation 33 Core treatment 14 Importing a Hessian file 35 Real space cutoff 15 Analyzing DMol3 results 35 Harris approximation 17 Updating structure 36 Solvation scheme 17 Displaying trajectory and chart data 37 Performance tips 18 Creating a trajectory and chart 37 Setting up k-points 18 Animating the trajectory 38 Setting up a geometry optimization 19 Chart Viewer point selection 38 Algorithms for the optimization 20 Visualizing volumetric data 38 Parameters for the optimization 20 Electron density 38 Electrostatic potential 39 Meta-GGA functionals 63 Fukui functions 40 Numerical basis sets 63 Molecular orbitals 40 Atomic basis sets are generated Field visualization 41 numerically 63 Visualizing Fermi surfaces 42 Advantages of numerically derived basis sets 63 Displaying population analysis results 42 Additional basis functions, including Displaying computed charges, spins, and polarization 63 bond orders 43 Numerical integration 65 Displaying band structure charts 43 Atomic and molecular integration grids 65 Displaying density of states charts 44 Integration points, atomic size, precision, Full density of states 45 and computational cost 65 Partial density of states 45 Atomic shells 66 Calculating elastic constants 46 Assuring consistent precision during Displaying the averaged potential chart for integration 66 work function calculations 46 Partition functions improve convergence Analyzing optical properties 47 and avoid nuclear cusps 66 Displaying Raman spectra 48 Pseudopotentials 67 Calculating reaction kinetics 48 Norm-conserving pseudopotentials 68 Displaying solvation properties 49 Evaluating the Coulombic potential Analyzing current and transmission numerically 69 properties 50 The model charge density 70 DMol3 jobs 51 Effect of angular truncation on precision Using DMol3 job control 51 of model charge density 70 Remote DMol3 jobs 51 The Coulombic potential 70 A sample DMol3 run 51 The total potential 70 Computational self-consistent field If a remote DMol3 job fails 53 procedure 70 Running DMol3 in standalone mode 54 Interpolating the numerical atomic bases DMol3 file formats 57 onto the molecular grid 70 DMol3 file formats - ARC 58 Constructing the initial molecular electron DMol3 file formats - BANDS 58 density 71 DMol3 file formats - CAR and MDF 58 Additional computational costs 71 DMol3 file formats - COSMO 58 Reducing the computational cost 71 DMol3 file formats - GRD 59 Damping and convergence 71 DMol3 file formats - HESSIAN 59 Efficiently calculating the electrostatic potential 71 DMol3 file formats - HESSWK 59 Effect of auxiliary density approximation DMol3 file formats - INPUT 60 on accuracy of calculated total energy 72 DMol3 file formats - OCCUP 60 SCF convergence acceleration by DIIS 72 DMol3 file formats - OUTMOL 60 Energy gradients 73 DMol3 file formats - PDOS_WEIGHTS 61 Predicting chemical structure 73 DMol3 file formats - TPVEC 61 First derivative of total energy with DMol3 file formats - TPDENSK 61 respect to change in nuclear position 73 Reaction Kinetics Study Table 61 Derivative of the basis function 74 Theory in DMol3 62 Derivation of other terms 74 Density functional theory (DFT) in DMol3 62 The final equation for the derivative of the Functionals in DMol3 62 energy 75 Local functionals 62 Computational costs 75 Nonlocal functionals 62 Potential problems 75 Hybrid functionals 62 Minimization algorithms; molecular DMol3 TS Optimization dialog 105 symmetry 75 DMol3 TS Confirmation dialog 105 Electronic excitations with TD-DFT 75 DMol3 Elastic Constants dialog 106 Predicting UV-Vis spectra 75 DMol3 Reaction Kinetics dialog 107 Computational costs 76 DMol3 Transport dialog 109 Accuracy of excitation energies and orbital Setup tab 110 overlap 77 Density Mixing 110 TD-DFT in combination with hybrid functionals in DMol3 77 Electrode 111 Molecular dynamics 77 DMol3 Transmission dialog 111 Ensembles 77 DMol3 Current/Voltage dialog 111 NVE ensemble 78 Electrodes tab 111 NVT dynamics 78 Electrostatics tab 112 Constraints 79 DMol3 Poisson Boundary Conditions dialog 112 Point group symmetry 80 Electronic tab 113 COSMO-solvation effects 80 DMol3 Electronic Options dialog 115 DMol3/COSMO 82 SCF tab 116 Determination of the cavity surface (or solvent-accessible surface) 83 k-points tab 117 Determination of non-electrostatic Orbital Cutoff tab 118 contributions to the free energy of Solvent tab 119 solvation 83 DFT-D tab 120 COSMO-SAC model 83 Properties tab 121 COSMO sigma profile 84 Band structure selection 122 Electric field gradients 84 Density of states selection 122 Thermodynamic calculations 86 DMol3 Density of States Options Enthalpy 86 dialog 123 Entropy 87 Electron density selection 124 Heat capacity 87 Electrostatics selection 125 Using the results 88 Frequency selection 125 Fitting atomic point charges to the Partial Hessian dialog 126 electrostatic potential (ESP) 88 Fukui function selection 127 Mulliken and Mayer bond orders 89 Optics selection 127 Hirshfeld charge analysis 90 DMol3 Optics Options dialog 128 Fukui functions 91 Orbitals selection 129 Raman spectra 92 Population analysis selection 129 Basis set superposition error 93 DMol3 Grid Parameters dialog 130 Converging SCF 93 Job Control tab 131 Challenging systems 94 DMol3 Job Control Options dialog 132 Checklist 94 DMol3 Job Files dialog 133 Dialogs in DMol3 96 DMol3 Analysis dialog 133 DMol3 Calculation dialog 96 Band structure selection 134 Setup tab 96 Current/Voltage selection 135 DMol3 Energy dialog 99 Density of states selection 136 DMol3 Geometry Optimization dialog 100 DMol3 DOS Analysis Options dialog 137 DMol3 Dynamics dialog 101 Elastic constants selection 138 Dynamics tab 102 Electron density selection 138 Thermostat tab 102 Energy evolution selection 139 DMol3 Transition State Search dialog 103 Fermi surface selection 139 Fukui function selection 140 Optics selection 141 DMol3 Optics Analysis Options dialog 141 Orbitals selection 142 Population analysis selection 143 Potentials selection 144 Raman spectrum selection 144 Reaction kinetics selection 145 Solvation properties selection 146 Choose COSMO File dialog 146 Structure selection 147 Thermodynamic properties selection 147 Transmission selection 148 DMol3 keywords 149 DMol3 References 150 DMol3 Introduction DMol3 allows you to model the electronic structure and energetics of molecules,