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Jaguar User's Guide JAGUAR USER’S GUIDE Version 4.2 March 2002 Julie R. Wright © 1998, 2000, 2001, 2002 Schrödinger, Inc. All Rights Reserved. JAGUAR USER’S GUIDE Version 4.2 March 2002 Julie R. Wright Schrödinger, Inc. 1500 SW First Avenue, Suite 1180 Portland, OR 97201 Telephone: (503) 299-1150 Fax: (503) 299-4532 Email: [email protected] © 1998, 2000, 2001, 2002 Schrödinger, Inc. All rights reserved. Copyright © 1998, 2000, 2001, 2002 Schrödinger, Inc. All rights reserved. Schrödinger, Inc. provides this publication “as is” without warranty of any kind, either expressed or implied. NBO 4.0 is copyright © 1996 Board of Regents of the University of Wisconsin System on behalf of the Theoretical Chemistry Institute. Babel 1.3 is copyright © 1992-96 W. Patrick Walters and Matthew T. Stahl. SPARTAN is a trademark owned by Wavefunction, Inc. BIOGRAF and Cerius2 are trademarks of Molecular Simulations, Inc. Gaussian, Gaussian 90, Gaussian 92, and Gaussian 94 are federally registered trademarks of Gaussian, Inc. Silicon Graphics, IRIX, and OpenGL are trademarks of Silicon Graphics, Inc. IBM is a registered trademark of International Business Machines Incorporated. DEC is a trademark of Digital Equipment Corporation. UNIX is a registered trademark of UNIX Systems Laboratories, Inc. X Window System is a registered trademark of Massachusetts Institute of Technology. All other brand or product names are trademarks or registered trademarks of their respective companies or organizations. 420067032002 Table of Contents Jaguar User’s Guide 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 Z-Matrix Format for Geometry Input ................................................................. 11 Variables and Dummy Atoms in Z-Matrix Input ............................................... 13 Constraining Z-Matrix 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 Table of Contents i Jaguar User’s Guide Table of Contents 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 ...............................................................................
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