Table of Contents
1. Introduction 1
1.1. Overview of this User's Guide 1
1.2. Citing Jaguar in Publications 3
1.3. Technical Support 3
2. Using Jaguar's Interface 4
2.1. Sample Calculation 5
2.2. Molecular Structure Input 8
Inputting or Editing a Geometry Within the Interface 8
Cartesian Format for Geometry Input 9
Variables in Cartesian Input 10
Constraining Cartesian Coordinates 10
ZMatrix Format for Geometry Input 11
Variables and Dummy Atoms in ZMatrix Input 13
Constraining ZMatrix Bond Lengths or Angles 14
Counterpoise Calculations 15
Specifying Coordinates for Hessian Refinement 15
2.3. Charge and Multiplicity (State) 16
2.4. Reading Files 16
Reading a Geometry, But No Calculation Settings 17
Reading In Both Geometries and Job Settings 19
Read as Geometry 2 or Geometry 3 Settings 19
2.5. Geometry Display 19
Display Window Basics: Orientation & Mouse Control 20
Display Styles 21
Labels 22
Other Display Options 22
Choosing a Structure To Display 23
Closing the Display Window 23
2.6. Cleaning up Molecular Geometries 23
The Cleanup Button 23
The Symmetrize Molecule Button 24
Tolerance 25
Finding the Point Group 25
Symmetrizing Coordinates 26
2.7. Running Jobs and Saving Input 26
Starting Individual Jobs from the Interface 26
Running Batch Jobs or Scripts from the Interface 29
Saving Input Files 31
Output 32
2.8. Other Interface Features 32
Checking Jobs with the Job Status Window 33
Resetting and Quitting 33
About and Help Buttons 34
Editing Input 34
Other Main Window Options 35
3. Options 37
3.1. Density Functional Theory (DFT) Settings 38
Stage and Grid Density 38
Method Options 39
Functionals 40
3.2. Local MP2 Settings 41
Summary of the LMP2 Method in Jaguar 42
Setting Up an LMP2 Calculation 43
3.3. Generalized Valence Bond (GVB) Settings 44
GVB or GVB-RCI Pair Input 44
3.4. GVB-LMP2 Calculations 45
3.5. Solvation 46
Solvent Parameters 47
Performing or Skipping a Gas Phase Optimization 48
3.6. Properties 48
Electrostatic Potential Fitting 49
Multipole Moments 50
Polarizability and Hyperpolarizability 50
Electron Density 51
Mulliken Population Analysis 51
Natural Bond Orbital (NBO) Analysis 52
3.7. Frequencies & Related Properties 52
Frequencies 53
Atomic Masses 53
Scaling of Frequencies 54
Infrared Intensities 54
Thermochemical Properties 55
3.8. Basis Set 56
3.9. Methods 60
Wavefunction Type (Restricted or Unrestricted) 60
Choosing an Initial Guess Type 61
Convergence Issues 62
Accuracy Level 63
Analytic Corrections 64
Final Localization of the Orbitals 64
Symmetry 65
4. Optimizations and Scans 66
4.1. Geometry Optimization: The Basics 66
Maximum Iterations (Number of Structures Generated) 67
Geometry Convergence Issues 67
The Initial Hessian 68
Trust Radius 69
4.2. Constraining Coordinates 69
Freezing All Bond Lengths, Bond Angles, or Torsional Angles 69
Freezing Specific Coordinates 70
Applying Constraints by Using Variables 71
4.3. Transition State Optimizations 72
Transition State Search Method 72
Specifying Different Structures for the Reaction 73
Initial LST Guess 74
Searching Along a Particular Path or Eigenvector 75
Eigenvector Following 76
Refinement of the Initial Hessian 76
Specifying Coordinates for Hessian Refinement 77
4.4. Geometry Scans 78
5. Output 80
5.1. Summarizing Jaguar Results 80
Reporting Final Results from One or More Jobs 81
Reporting Intermediate Results 83
Reporting Results for Each Atom 84
5.2. Output from a Standard HF Calculation 85
5.3. Output File Changes for Calculation Options 90
DFT 90
LMP2 91
GVB 91
GVB-RCI 93
Geometry or Transition State Optimization (HF, GVB, DFT, and LMP2) 93
Optimizations with GVB-RCI Wavefunctions 97
Solvation 98
Geometry Optimization in Solution 102
Properties 102
Frequency, IR Intensity, and Thermochemistry Output 106
Basis Set 107
Methods 108
5.4. Standard Output Options 108
echo input file and parameter list 108
memory, disk, and i/o information 109
detailed timing information 109
geometries in atomic units also 109
multipole moments in atomic units also 109
bond lengths and angles 109
connectivity table 110
overlap matrix 110
geometry optimization details 110
one-electron Hamiltonian 110
Gaussian function list (basis set) 111
Gaussian function list (derivatives) 114
5.5. Files Output Options 114
Gaussian-92 input deck (.g92) 114
GAMESS input file (.gamess) 115
SPARTAN archive file (.arc) 115
Gaussian-92 basis set (.gbs) 115
XYZ file (.xyz) 115
Molden orbitals file (.molf) 115
5.6. Output Options Per Iteration 115
energy components 116
density matrix 116
All J and K matrices, AO space 116
Fock matrix in AO (HF) or MO (GVB) space 117
Fock matrix in CO space 117
GVB data: f, a, b, ci coefficients, etc. 117
5.7. Output Options for Orbitals 117
When: 118
What: 119
How: 119
5.8. The Log File 122
6. Tips and Suggestions 124
6.1. Customizing Interface Settings: The jaguar.hosts File 124
6.2. Customizing the Interface Appearance 127
6.3. Tips for Various Types of Jobs 127
Organometallics and Other Difficult-to-Converge Systems 128
GVB Calculations: GVB Pair Selection 130
Geometry Optimization 130
Electrostatic Potential Charge Fitting 131
6.4. Restarting Jobs and Using Previous Results 131
Finding the Restart File in the Temp Directory 132
6.5. Using Jaguar with MOPAC 133
Running MOPAC 133
Adding MOPAC Geometries to Jaguar Input 134
Using MOPAC Hessians in Jaguar Input 134
Specifying Different File Names 135
6.6. Suggestions for Gaussian Users 136
Generating Gaussian Input Files with Jaguar 136
Getting Basis Sets or Orbitals for Gaussian 138
Using Gaussian Files as Jaguar Input 138
7. Theory 139
7.1. The Pseudospectral Method 139
7.2. Pseudospectral Implementation of the GVB Method 142
7.3. GVB-RCI Wavefunctions 146
7.4. Pseudospectral Local MP2 Techniques 148
7.5. Density Functional Theory 152
8. The Jaguar Input File 154
8.1. The jaguar Command 154
Selecting a Calculation Host 155
Selecting Particular Jaguar Executables 156
Running a Jaguar Job from the Command Line 156
Killing a Jaguar Job 158
8.2. General Description of the Input File 159
Sections Describing the Molecule and Calculation 160
8.3. The zmat, zmat2, and zmat3 Sections 162
8.4. The zvar, zvar2, and zvar3 Sections 164
8.5. The coord and connect Sections 165
8.6. The gen Section 166
Geometry Input Keywords 167
Molecular State Keywords (Charge and Multiplicity) 167
Atomic Mass Keyword 167
Symmetry-Related Keywords 168
GVB and Lewis Dot Structure Keywords 169
LMP2 Keywords 171
DFT Keywords 173
Geometry Optimization and Transition State Keywords 177
Solvation Keywords 183
Properties Keywords 185
Frequency-Related Keywords 188
Basis Set Keywords 190
Keywords for SCF Methods 191
Initial Guess Keywords 195
Localization Keywords 197
Using Babel to Output Files 199
Standard Output Keywords 201
Files Output Keywords 203
Output Keywords for Each Iteration 204
Orbital Output Keywords 205
Grid and Dealiasing Function Keywords 207
Memory Usage Keywords 209
8.7. The gvb Section 212
8.8. The lmp2 Section 213
8.9. The atomic Section 214
General Format of the atomic Section 214
Input Types That Specify Physical Properties 216
Basis, Grid, Dealiasing Function, and Charge Usage for Individual Atoms 217
Defining Fragments 218
8.10. The hess Section 219
8.11. The guess Section 220
8.12. The pointch Section 222
8.13. The efields Section 222
8.14. The ham Section 223
8.15. The orbman Section 223
8.16. The echo Section 225
8.17. The path Section 225
8.18. The plot Section 228
8.19. NBO Sections 229
8.20. Running Multiple Jobs: jaguar batch 230
Batch Input File Format 230
Batch Input File Example 233
Running "jaguar batch" 234
9. Other Jaguar Files 237
9.1. The Basis Set File 238
9.2. The Initial Guess Data File 242
9.3. The Dealiasing Function File 244
File Format and Description 245
Sample File 247
9.4. The Grid File 249
File Format and Description 249
9.5. The Cutoff File 253
9.6. The Lewis File 255
Describing Bonding Types in the Lewis File 257
Describing Hybridization Types in the Lewis File 258
Setting van der Waals Radii from Lewis File Data 260
Default Behavior for Setting Radii 264
10. Troubleshooting 266
10.1. Problems Getting Started 266
The SCHRODINGER Environment Variable 267
Including the jaguar Command in Your Path 268
Problems Starting the Interface 268
Problems Related to Your Temporary Directory 270
Problems Running Jaguar Calculations on Other Nodes 271
10.2. On-Line Help 273
10.3. Other Problems 273
11. The Parallel Jaguar Module 277
11.1. About Parallel Jaguar 277
11.2. Installing Parallel Jaguar 277
11.3. Requirements for Different Computer Platforms 278
SGI 278
LINUX 279
IBM 282
HP, Compaq, Sun 284
11.4. Running Jobs In Parallel 284
12. The pKa Prediction Module 287
12.1. Introduction 287
12.2. Theory of pKa Calculation 289
Ab initio Quantum Chemical Calculation of pKa's 289
Empirical Corrections 292
12.3. Predicting pKa's in Complex Systems 293
Overview 293
Conformational Flexibility 293
Equivalent Sites 295
Multiple Protonation Sites 295
12.4. Results 296
12.5. Guide to Running the Program 306
Installing the pKa Module 306
JAGUAR Input Files for pKa Calculations 306
Running pKa Calculations 307
Monitoring pKa Calculations 308
Initial Geometry 308
Information by Element 311
References 319
Index 329
Keywords 345