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Multiwfn: A Beginner’s Guide to Wavefunction Analysis

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How to Visualize Molecular Orbitals with Multiwfn and VMDVisualizing molecular orbitals helps chemists and materials scientists understand bonding, reactivity, and electronic structure. This guide shows how to generate molecular orbital cube files with Multiwfn and visualize them in VMD (Visual Molecular Dynamics). It covers required files, preparing wavefunction data, generating orbital grids, exporting cube files, rendering in VMD, and tips to make clear, publication-quality images.

What you’ll need

  • Multiwfn — a multifunctional wavefunction analysis program (command-line; available at multiwfn.codeplex/official distribution).
  • VMD (Visual Molecular Dynamics) — for 3D visualization and high-quality rendering.
  • A quantum chemistry output or formatted checkpoint file containing molecular orbitals and basis information. Common formats: Gaussian checkpoint (.fchk), Molden (.molden), GAMESS output, ORCA .gbw, etc. Multiwfn accepts many formats.

Step 1 — Prepare your wavefunction file

  1. Run your quantum chemistry calculation to obtain orbitals. For Gaussian, create a formatted checkpoint (.fchk) using:
    • Gaussian route: add “formchk” utility after the job to convert .chk → .fchk.
  2. Alternatively, export a Molden file (.molden) from your quantum chemistry package; Multiwfn reads Molden files directly.

Place the .fchk or .molden in the working directory where you’ll run Multiwfn.

Step 2 — Start Multiwfn and load the file

  1. Open a terminal and run Multiwfn by typing: 
    
multiwfn yourfile.fchk

    or 

    
multiwfn yourfile.molden
  2. Multiwfn will read the file and display a main menu. Note the molecule and basis details it reports to confirm successful loading.

Step 3 — Generate orbital grid data (cube file)

Multiwfn can produce Gaussian cube files containing orbital amplitudes on a 3D grid. Typical workflow inside Multiwfn:

  1. From the main menu select “6 — Plot cube file and grid data” (menu numbers may vary by Multiwfn version).
  2. Choose the option to output molecular orbitals to a cube file (often labeled “Export orbital to cube file” or similar).
  3. Select which orbital(s) to export:
    • For closed-shell systems: occupied orbitals often numbered from 1 to Nocc; virtual orbitals start after that.
    • You’ll be prompted for the orbital index (e.g., HOMO, LUMO). If you want HOMO, determine its index from Multiwfn’s orbital list or from your quantum chemistry output; you can also input negative indices in some versions (e.g., -1 for HOMO).
  4. Set grid extents and resolution:
    • Define the cube box size (center and dimensions) or let Multiwfn use an automatic box that fits the molecule.
    • Choose grid spacing (commonly 0.15–0.25 Å for publication-quality images; smaller spacing = higher quality but larger files/time).
  5. Choose whether to output only the positive/negative isosign or the full signed grid (for orbital phases you need signed data; VMD uses that to color lobes).
  6. Output filename: choose something like mol_orb_X.cube.

Example typical parameters:

  • Center: center of mass (auto)
  • Box size: auto or add padding ~3 Å beyond outer atoms
  • Grid spacing: 0.18 Å

Wait while Multiwfn computes the orbital values and writes the cube file.

Step 4 — Verify cube file (optional)

You can inspect the beginning of the cube file in a text editor: it includes header lines with the atom count, origin, grid dimensions, cell vectors, and atom coordinates with nuclear charges. This helps ensure the box and grid are correct.

Step 5 — Open the cube file in VMD

  1. Launch VMD.
  2. File → New Molecule → Browse → select the .cube file → Load.
  3. VMD loads the grid as a volumetric dataset and typically displays isosurfaces corresponding to an isovalue (default). Initially you might see nothing or a single isosurface; proceed to configure the display.

Step 6 — Create orbital isosurfaces in VMD

  1. Open the “Graphics” → “Isosurface” or use the “VolMap”/“Isosurface” plugin via the “Extensions” menu depending on VMD version.
  2. In the “Graphical Representations” window:
    • Drawing Method: Isosurface (or use “Isosurface” representation).
    • Select the loaded volume molecule (e.g., volmap) as the data source.
    • Set the isovalue: common starting isovalues are 0.02–0.05 e/Å^3 (but values depend on grid spacing and orbital normalization). Adjust until lobes appear at an aesthetically and chemically meaningful size.
    • Color by “Volume” or use a two-color scheme to show positive/negative phases. To show phases:
      • Use the “Coloring Method” → “Volume” and then under the Color Scale choose a red/blue or red/white/blue scale where positive values map to one color and negative to another.
    • Add two representations if needed: one for positive isovalue (e.g., +0.03) and one for negative (e.g., -0.03), assigning different colors to each.
  3. Render the molecular skeleton (atoms/bonds):
    • Load the molecular geometry (if not included) or use the atom coordinates embedded in the cube header.
    • Add a new representation for “Selection: all” with drawing method “Licorice” or “CPK” at suitable radii.
    • Adjust transparency of isosurfaces if desired.

Step 7 — Fine-tuning and styling

  • Lighting: use VMD’s “Display” → “Display Settings” to adjust ambient and specular lighting for better depth.
  • Background: switch to white or black depending on journal style (Display → Background).
  • Material: try “Transparent” or “Opaque” materials for different effects.
  • Isovalue consistency: when comparing multiple orbitals or molecules, use the same isovalue and grid spacing to make relative sizes meaningful.
  • Labels: use VMD’s “Graphics → Labels” to annotate orbital energies or orbital numbers.
  • Multiple orbitals: load several cube files and use consistent isovalues and colors for comparison.

Step 8 — Produce publication-quality images

  1. Use VMD’s “File → Render” with a high-quality renderer:
    • Tachyon (fast ray tracer) is included and produces good results.
    • For even higher quality, export to POV-Ray or use external ray tracers that VMD supports.
  2. Set image resolution: 300–600 dpi equivalent; for figures use 2000 px on the longest side or higher depending on journal requirements.
  3. Anti-aliasing and depth of field: enable in the renderer settings if available.
  4. Export transparent PNGs or high-resolution TIFFs depending on publisher requirements.

Command-line rendering example (Tachyon):

render tachyon internal image.tga

Then convert to PNG/TIFF with image tools if needed.

Tips and troubleshooting

  • If lobes look distorted or missing: increase grid resolution (smaller spacing) or enlarge the cube box.
  • If isosurfaces are choppy: decrease grid spacing or smooth via rendering options.
  • Colored phase inversion: ensure cube file preserves sign information (Multiwfn writes signed values by default for orbitals).
  • Large systems may produce huge cube files. Export only a region around the orbitals of interest, or use coarser grids when exploring before finalizing.
  • Batch generation: Multiwfn can be scripted to export multiple orbitals automatically—use its input scripts or call Multiwfn interactively with redirected input.

Example workflow (compact)

  1. Generate .fchk from Gaussian (or .molden from other QM package).
  2. Run: multiwfn molecule.fchk → choose Plot cube file → select orbital → set grid/spacing → write mol_orb_N.cube.
  3. Open mol_orb_N.cube in VMD → create isosurface representations for +iso and -iso → color red/blue → add atom/bond representations → render with Tachyon at high resolution.

Common pitfalls

  • Forgetting to export signed orbital data — phasing will be lost.
  • Using inconsistent isovalues when comparing orbitals.
  • Rough isosurfaces from coarse grids.
  • Overly large box resulting in wasted resolution.

Brief troubleshooting checklist

  • No isosurface visible: try lower isovalue or check that the cube file has nonzero values.
  • Wrong phase colors: confirm VMD is using the volume value for coloring and that you have positive/negative isovalue pairs.
  • Very large file sizes: increase grid spacing or restrict box to region of interest.

Using Multiwfn to create cube files and VMD to render them gives you a flexible, scriptable, and high-quality workflow for orbital visualization. With practice you can automate batch exports, standardize visual styles, and produce consistent figures for presentations and publications.

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