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GaussView 6 Features at a Glance

Features new to GaussView 6 are in blue; features enhanced in GaussView 6 are in green.

Examine Molecular Structures

  • Rotate, translate and zoom in 3D in any display using mouse operations and/or a precision positioning toolbar
  • View numeric value for any structural parameter
  • Use multiple synchronized or independent views of same structure (customizable)
  • Manipulate multiple structures as an ensemble
  • Display formats: wire frame, tubes, ball & stick/bond type, space fill (CPK) style
  • View per-atom labels for element, serial number, NMR shielding (when available)
  • Visualize depth with fog feature
  • Display stereochemistry info
  • Highlight, display or hide atoms based on rich selection capabilities (optionally persistent)

Build/Modify Molecules

  • Convenient palettes for atoms, functional groups, rings, amino acids (central fragment, amino- or carboxyl-terminated) and nucleosides (central fragment, C3’-, C5’-terminated, free forms)
  • Custom fragment libraries
  • Import standard molecule file formats:
    • PDB, including ones created by AMBER. Optionally include/discard waters, apply standard residue bonding on PDB import.
    • Gaussian input (.gjf and .com), output (.log), checkpoint (.chk and .fchk), cube (.cub), and frequency (.gfrq) files
    • Sybyl .mol2, .ml2.; include/convert .mol2 lone pairs
    • MDL files: .mol, .rxn, .sdf
    • Crystallographic Information files: .cif
    • Optionally include intermediate structures from optimizations, scans, etc.
  • Accurately add hydrogens automatically or manually to an entire molecule or a selection
  • An advanced open dialog, allowing options to be customized and retained across sessions:
    • Reading intermediate geometries
    • Using the bond table and weak bond inclusion
    • Gaussian input & log file load orders
    • PDB and .mol2 file settings
    • Saving the formatted checkpoint file
  • Modify bond type/length, bond angles, dihedral angles
  • Rationalize structures with an advanced clean function
  • Recompute bonding on demand
  • Increase or decrease symmetry of molecular structure; constrain structure to specific point group
  • Mirror invert structure
  • Invert structure about selected atom
  • Place atom/fragment at centroid of selected atoms
  • Define named groups of atoms via:
    • Click, marquee, & brush selection modes
    • Complex filters combining atom type, number, MM settings, ONIOM layer
    • Select by PDB residue and/or secondary structure (e.g., helix, chain)
    • Expand selections by bond or proximity
    • Use groups for display purposes and in Gaussian input
  • Specify nonstandard isotopes
  • Customize fragment placement behavior
  • Specify custom bonding parameters

Graphical Setup for Specific Calculations

Specify input for complex calculations via simple mouse/spreadsheet operations:

  • Build unit cells for polymers, 2D surfaces and crystals (periodic boundary conditions)
    • Constrain to specific space group symmetry
  • Assign atoms to ONIOM layers by
    • Direct selection
    • Bond proximity to specified atom
    • Absolute distance from specified atom
    • PDB file residue, secondary structure
    • Complex selection criteria
  • View/specify MM atom types and charges
  • Add/redefine redundant internal coordinates
  • Specify frozen atoms/coordinates during optimizations
  • Set atom equivalences for QST2/QST3 TS optimizations
  • Manipulate MOs: Select, rearrange/reoccupy orbitals for CASSCF, etc.
  • Define fragments for fragment guess/counterpoise calculations
    • Assign fragment-specific charges and spin multiplicities
  • Include PDB data in molecule specification
  • Select normal modes for frequency calculations
  • Specify atoms for NMR spin-spin coupling
  • Search for conformations using the GMMX add-on
  • Full AMPAC integration if software is installed

Prepare and Run Gaussian Calculations

  • Create input files via a menu-driven interface:
    • Select job/method/basis from pop-up menus; related options appear automatically
    • Supports all major Gaussian 16 features
    • Convenient access to commonly-used general options
    • Additional input can be entered; input sections in imported files are retained
    • Preview input file before saving/submitting
  • Select solvent and specify other parameters for calculations in solution
  • Specify Link 0 commands
  • Specify settings for multiprocessor and cluster/network parallel jobs
  • Use calculation schemes to set up jobs from templates
  • “Quick launch” Gaussian jobs with a single mouse click
  • Molecule specification created automatically
    • Optional connectivity section
  • Monitor/control local Gaussian and utility processes
  • Integrated, customizable queuing system
  • Stream log files in a text-searchable window
  • Initiate remote jobs via a script
  • Generate job-specific input automatically
    • PBC translation vector for periodic structures like polymers and crystals
    • Orbital alterations
    • Multiple molecule specifications for QST2/QST3 transition state searches
    • Fragment guess and counterpoise per-fragment charge and spin multiplicity
  • Apply calculation settings to a group of molecules with one click
  • Save/submit identical jobs for a group of molecules in a single step, using unique file names

Examining and Visualizing Gaussian Results

  • Select which jobs to open from multi-step results files
  • Show calculation results summary, including basic information, optimization step data and thermochemical results
  • Display results tables for a molecule group
  • Examine atomic charges: numerical values, color atoms by charge, dipole moment vector
  • Visualize atomic properties, predicted bond lengths and predicted bond orders
  • Create surfaces and contours for molecular orbitals, electron density, electrostatic potential, spin density, NMR shielding density
    • Display formats: 3D solid, translucent or wire mesh; 2D contour
    • Color surfaces by a separate property
    • Specify the desired contour plane
    • Load cubes created by Gaussian; save computed cubes for future reuse; perform operations on cubes
  • Animate normal modes:
    • Indicate motion via displacement vector, dipole derivative unit vector
    • Displace structures along normal mode
    • Select subset of modes for display
    • Save generated normal modes back to checkpoint file
    • Scale frequencies
    • Save animations as MP4 movies, with options for speed, aspect ratio, looping, time delay between frames and frames/loop
  • Display spectra: IR, Raman, NMR, VCD, ROA, UV-Visible, etc.
    • Select Harmonic and/or Anharmonic results
    • Customize plot displays
    • Display multiple data sets on a single spectra plot, with optional conformational averaging
  • Substitute isotopes in frequency analysis
  • Specify incident light frequency for frequency-dependent calculations
  • Display results from Gaussian trajectory calculations
  • View energy plot of conformational search result set
  • NMR Results:
    • Report absolute NMR chemical shifts or relative to reference compound
    • Export NMR summary data as text
  • Animate structure sequences: geometry optimizations, IRC reaction paths, potential energy surface scans, BOMD and ADMP trajectories
    • Single play or continuous looping; play in reverse
    • Save animations as MP4 movies, with options for speed, aspect ratio and frame & endpoint delays
    • Plots of related data are also produced
  • Display 3D surface plots for 2-variable scan calculations
  • Customize plot and spectra displays by zooming, scaling, inverting, etc.
    • Add molecular properties to plots
    • Advanced plot customization; line color, canvas and background color, title, x- and y- axis settings, etc.
    • Mixture Editor for multiple overlaid plots
  • Save any image to a file (including customizations):
    • Produce web graphics: JPEG, PNG and other formats
    • Produce publication quality graphics files and printouts: TIFF, JPEG, vector graphics EPS
    • Create images at arbitrary size and resolution
    • Select full color or high quality grey scale formats
    • Specify custom colors and/or background
  • Save plots as images or textual data files
  • Save animations in GIF, MNG, MP4 format or as individual frames
  • Display PCM solvation cavity as a surface

Customize GaussView

Set/save preferences for most aspects of GaussView functionality:

  • Control building toolbars individually
  • Colors: per-element, molecule window background, surfaces, transparency
  • Builder operation: atom and fragment join methods, adding hydrogens when needed, automated full or partial clean operations, etc.
  • Gaussian 16 calculation settings
  • Gaussian job execution methods
  • Display modes
  • Window placement and visibility
  • Icon sizes
  • File/directory locations
  • Image capture and printing defaults
  • Animation settings and movie defaults
  • Clean function parameters
  • Charge distribution display defaults
  • Custom bonding parameters
  • GaussView Tips facility
  • Windows file extension associations
  • Context sensitive help

Last updated on: 15 June 2017.