gqteaWinToga

gqteaWinToga

A Windows toolkit for preparing, visualizing and analyzing molecular simulations.

Build inputs for CPMD, Quantum ESPRESSO cp.x, ORCA and surface hopping runs, then turn the trajectories they produce into bond distributions, radial distribution functions, residence times, power spectra and rate constants. From Gaussian wavefunctions, map the electrostatic potential onto molecular surfaces and find the reactive sites of a molecule with Fukui functions, all from one window.

Download for Windows

Free and open source, MIT license. Windows 10 or 11, 64-bit.

Release notes and earlier versions

Glycine with two hydrogen-bonded waters. Drag to rotate.

What's inside

The program's main window groups its tools into five tabs. Each tool opens its own window: choose your files, enter the parameters, and run.

Measure geometry along a trajectory, usually a CPMD TRAJEC.xyz, and get averages, distributions and free-energy profiles.

  • Bond length analysis
  • All bond distances at once, solute only or the whole system
  • Bond angle and all bond angles
  • Dihedral angle and all dihedral angles
  • Hydrogen bond analysis
  • Comparison of geometric parameters between two runs, for example isolated versus solvated, with MAE and RMSD

Since version 0.7.5

Electrostatic potential on molecular surfaces

Open a Gaussian formatted checkpoint (.fchk or .fch, made with formchk). The tool builds one or more electron-density isosurfaces, computes the electrostatic potential exactly at every surface point, and finds its maxima and minima the way Multiwfn does. The result is drawn the way GaussView draws a mapped ESP: red where the potential is negative, blue where it is positive.

  • Two quantities, kept apart. The surface is set by the electron density (default isovalue 0.0004 a.u.; several isovalues per run); the potential is what is mapped onto it, in a.u. or kcal/mol.
  • Exact potential. Analytic integrals over the Gaussian basis set (s to g functions, closed or open shell), matching Gaussian’s own cubegen to better than 10−6 a.u. If cubegen is installed, it can be used instead.
  • Surface extrema saved. Every global and local maximum and minimum, with its value in a.u. and kcal/mol, its position in Å, the nearest atom and the isovalue of its surface, goes to <name>_ESP_extrema.txt.
  • Fast. A small molecule takes a second or two; the optional numba package makes larger ones about five times faster.
  • Ready for a paper. Choose a black, white or grey background and export the 3D view as a PNG image.

How to use it · The equations and methods

Ethylene electrostatic potential mapped on its electron-density surface: red over the centre of the carbon-carbon double bond, green on most of the surface, cyan to blue toward the hydrogen atoms, with a colour bar from -2.097e-2 to 2.097e-2 atomic units across the top.
Ethylene, B3LYP/6-31G, on the ρ = 0.0004 a.u. surface. The π cloud is negative (−13.2 kcal/mol at the cyan minimum marker); the hydrogens are positive (orange maximum markers).

New in version 0.8.0

Fukui functions: where a molecule reacts

Give the tool three Gaussian .fchk files of one molecule at one geometry: the neutral molecule (N electrons), its anion (N+1) and its cation (N−1). It computes the Fukui functions from the three electron densities and shows where an added electron goes and where a removed one comes from. In other words, it shows which atoms favour nucleophilic, electrophilic or radical attack.

  • All the conceptual-DFT descriptors. f+, f−, f0 and the dual descriptor on a 3D grid, saved as cube files; the global indices (ionization potential, electron affinity, electronegativity, hardness, softness, electrophilicity and nucleophilicity); and the same functions condensed to each atom.
  • No external program needed. The atom-condensed indices come from built-in Hirshfeld charges for elements H to Ar. They agree with Multiwfn to within 3×10−4, and the 3D functions agree with Multiwfn’s cube files to within 10−5 a.u.
  • Seen in 3D. Show each function as positive and negative isosurfaces, or mapped in colour on the molecule’s density surface with its maxima and minima. Atoms can be drawn as lines, balls and sticks, or space-filling spheres, with or without their numbers.
  • Checked before computing. The tool refuses files with different atoms, geometries, basis sets or methods, and it says why. Phenol takes about eight seconds; the optional numba package makes the density grid about four times faster.

Prepare the three calculations

The new Gaussian Fukui Input Builder (Inputs tab) writes one Gaussian 16 input with three linked jobs: it optimizes the neutral molecule, then runs the anion and the cation as single points at exactly that geometry. It also writes a formchk script that converts the checkpoint files into .fchk files. You must enter the spin multiplicity of every state, because the builder never guesses one. When you then pick the neutral molecule’s file in the analysis tool, the anion and cation files are filled in for you. The input builder is in the source code now and will be in the next installer release.

How to use it · How to read the figure · The equations and methods

Phenol drawn as balls and sticks, seen face-on with the OH group at the top, under f-plus isosurfaces: large blue lobes over the four ring carbons beside and next-but-one to the carbon bearing OH, small red regions near that carbon, the carbon opposite it and the oxygen, and small blue caps on the hydrogens. A colour bar from -5.000e-3 to 5.000e-3 runs across the top.
Phenol, B3LYP/6-31G(d): f+ at ±0.005 a.u. Blue marks where an added electron goes. The large lobes sit on the ortho and meta carbons (condensed f+ ≈ 0.13 each), the sites most open to nucleophilic attack. Red marks where the other electrons move away.

Install

  1. Download the installer

    Use the download button above. You get a zip file named like gqteaWinToga-v0.8.0-INSTALLER.zip.

  2. Extract it

    Right-click the zip, choose Extract All, and open the extracted folder.

  3. Run the installer

    Double-click gqteaWinToga-…-INSTALLER.exe. It installs for your user account, so administrator rights are not needed. If Windows shows “Windows protected your PC”, choose More info, then Run anyway. The warning appears because the program isn't signed with a commercial certificate.

  4. Start the program

    Open gqteaWinToga from the Start menu, or from the desktop shortcut if you chose to create one.

Learn to use it

The user manual describes every tool, its input files and outputs, with worked examples such as finding a bond-length free-energy minimum, preparing a CPMD collision restart, grouping surface hopping frames by electronic state, locating the electrostatic potential minima of a molecule and reading a Fukui function figure of phenol.

Found a bug or have a request? Open an issue on GitHub.

Who makes it

gqteaWinToga is developed by the Grupo de Química Teórica e Estrutural de Anápolis (gQTEA) at the State University of Goiás (UEG), Brazil, for research and graduate teaching in computational chemistry.

  • Ademir J. Camargo
  • Valter H. C. Silva
  • Solemar S. Oliveira
  • Hamilton B. Napolitano
  • Luciano Ribeiro
  • Flavio O. Sanches

Contact: ajc@ueg.br