QuickIce

A portable GUI application for generating ice structures, ice-water interfaces, hydrate systems, export to full GROMACS-ready format, providing an interface for basic GenIce2 functions with more focus on gromacs input preparation.

Experimental

• This is a "pure vibe coding project" created as a coding exercise.
• While I (the human) attempted to review every single reference manually, please report to me for any incorrect citations that I didn't catch or critical flaws in the implemented methods.

Overview

What is QuickIce?

QuickIce v4.5 provides a 6-tab GUI workflow for generating molecular dynamics starting structures:

• Ice Generation — 11 ice polymorphs from thermodynamic conditions
• Hydrate Generation — Clathrate structures (sI, sII, sH) with guest molecules
• Interface Construction — Ice-water boundaries for surface studies
• Custom Molecule Upload — User-provided molecules in liquid phase
• Solute Insertion — THF/CH₄ concentration-based placement
• Ion Insertion — NaCl concentration-based placement

All exports are GROMACS-ready with TIP4P-ICE water model and bundled force field parameters.

Key Features:

• Interactive phase diagram with 11 ice polymorphs
• Real-time 3D molecular visualization (VTK)
• Side-by-side candidate comparison
• Multiple export formats (PDB, GROMACS .gro/.top/.itp, PNG, SVG)
• Unified keyboard shortcut for export (Ctrl+S)
• Multi-molecule GROMACS topologies

Binary Distribution (No Installation Required)

Pre-built executables are available for Linux and Windows. No Python or conda setup needed.

Quick Start:

• Linux: Download, extract, run ./quickice-gui
• Windows: Download, extract, double-click quickice-gui.exe

Details: See README_bin.md for download links and usage instructions.

Installation

System Requirements

Linux:

• GLIBC 2.28 or higher (Ubuntu 20.04+, Debian 10+, Rocky/RHEL 8+)
• 64-bit architecture
• OpenGL support for 3D visualization

Prerequisites

• Conda (Miniconda or Anaconda)

One-Time Setup

# Create conda environment
conda env create -f environment.yml

# For each new shell
source setup.sh

# Verify installation
python -m quickice --help

For detailed GUI documentation, see docs/gui-guide.md.

For CLI usage, see docs/cli-reference.md.

Quick Start (GUI)

Launch the GUI

python -m quickice --gui

Or for direct GUI access (bypasses router):

python -m quickice.gui

5-Minute Workflow

1. Generate Ice (Tab 0) — Click on phase diagram or enter T/P/N → Generate → View ranked candidates
2. Build Interface (Tab 2) — Select mode (slab/pocket/piece) → Generate interface → View ice/water phases
3. Insert Molecules (Tabs 3-5) — Upload custom molecule (Tab 3) OR set solute concentration (Tab 4) OR set ion concentration (Tab 5)
4. Export — Press Ctrl+S for GROMACS export from active tab

Example workflow:

• Tab 0: Generate Ice Ih at 273K, 0.1 MPa
• Tab 2: Build slab interface (ice-water-ice layers)
• Tab 4: Insert THF solutes at 0.5 M concentration
• Tab 5: Insert NaCl ions at 0.15 M concentration
• Ctrl+S: Export multi-molecule GROMACS files

Entry Point

QuickIce uses python -m quickice as the unified entry point:

• No arguments — Show help (like git with no args)
• Computation flags (-T, --interface, etc.) — CLI mode automatically
• --cli — Force CLI mode (skip PySide6 import, useful in CI)
• --gui — Force GUI mode (requires PySide6 + display)
• python quickice.py — Backward compatible, delegates to unified router

Features (6-Tab Workflow)

Tab 0: Ice Generation

Generate ice crystal structures from thermodynamic conditions:

• 11 ice polymorphs — Ih, Ic, II, III, V, VI, VII, VIII, IX, XV, X
• Interactive phase diagram — Click to select T/P conditions
• 10 ranked candidates — Energy-based ranking with diversity
• Real-time 3D viewer — Ball-and-stick, stick, VDW styles
• Hydrogen bonds — Dashed line visualization

Tip: Click on the phase diagram to populate temperature/pressure inputs automatically.

Tab 1: Hydrate Generation

Generate clathrate hydrate structures with guest molecules:

• Structure types — sI, sII, sH
• Guest molecules — CH₄ (methane), THF (tetrahydrofuran)
• Cage occupancy — Configure guest occupancy per cage type
• Supercell size — Set unit cell repetitions
• Dual-style rendering — Water lines + guest ball-and-stick

Export includes bundled GAFF2 parameters for guest molecules.

Tab 2: Interface Construction

Build ice-water interfaces for molecular dynamics simulations:

• Slab mode — Layered ice-water boundaries (ice | water | ice)
• Pocket mode — Water cavities within ice (sphere/cubic)
• Piece mode — Ice crystals embedded in water
• Phase-distinct visualization — Cyan ice, cornflower blue water
• PBC-aware collision detection — Automatic overlap removal

Generate ice candidates in Tab 0 first. Tab 2 uses candidates from Tab 0.

Tab 3: Custom Molecule Upload

Insert user-provided molecules into liquid water:

• File upload — Load .gro (coordinates) and .itp (topology) files
• Two placement modes:
  • Random — Automatic placement with overlap checking
  • Custom — User-specified position and rotation (Euler angles)
• Validation — Atom count check, residue name verification
• Distinct rendering — Unique colors per molecule type

Requires interface structure from Tab 2. User-provided .itp must include [ atomtypes ] section.

Tab 4: Solute Insertion

Insert THF or CH₄ solutes into liquid water:

• Concentration-based — Input mol/L → automatic molecule count
• Solute types — THF (tetrahydrofuran), CH₄ (methane)
• Source selection — Use interface from Tab 2 or custom molecules from Tab 3
• All-atom overlap checking — Prevents atom clashes
• Distinct rendering — CPK coloring for multi-atom molecules

Molecule count formula: N = concentration × liquid_volume × Avogadro

Tab 5: Ion Insertion

Insert Na⁺/Cl⁻ ions into liquid water:

• Concentration-based — Input mol/L → automatic ion count
• Source selection — Interface, custom molecule, or solute structures
• Charge neutrality — Equal Na⁺/Cl⁻ with Madrid2019 parameters (±0.85e) [Madrid2019]
• Automatic overlap removal — Prevents ion-water clashes
• VDW sphere rendering — Gold Na⁺, green Cl⁻

Requires structure from Tab 2, Tab 3, or Tab 4.

GROMACS Export

QuickIce exports GROMACS-ready files with unified keyboard shortcut:

Unified Export (Ctrl+S)

Press Ctrl+S from any tab to export the current structure:

Active Tab	Export Action	Files Generated
Tab 0	Ice GROMACS	.gro, .top, tip4p_ice.itp
Tab 1	Hydrate GROMACS	.gro, .top, tip4p_ice.itp, ch4_hydrate.itp/thf_hydrate.itp
Tab 2	Interface GROMACS	.gro, .top, tip4p_ice.itp
Tab 3	Custom Molecule GROMACS	.gro, .top, tip4p_ice.itp, custom.itp
Tab 4	Solute GROMACS	.gro, .top, tip4p_ice.itp, ch4_liquid.itp/thf_liquid.itp
Tab 5	Ion GROMACS	.gro, .top, tip4p_ice.itp, ion.itp

Molecule Ordering

Multi-molecule topologies follow GROMACS convention:

[ molecules ]
SOL               5919    ; Water molecules
CH4_H             128     ; Hydrate guests (from Tab 1)
THF_L             45      ; Liquid solutes (from Tab 4)
CUSTOM_MOL_1      10      ; Custom molecules (from Tab 3)
NA                12      ; Ions (from Tab 5)
CL                12

Order: SOL → hydrate guests → solutes → custom molecules → ions

Water Model

All exports use TIP4P-ICE water model:

Abascal, J. L. F., Sanz, E., García Fernández, R., & Vega, C. (2005).
A potential model for the study of ices and amorphous water: TIP4P/Ice.
Journal of Chemical Physics, 122(23), 234511.
DOI: https://doi.org/10.1063/1.1931662

Guest Molecule Parameters

CH₄ and THF use GAFF2 force field with RESP2(0.5) partial charges:

• Prepared with Sobtop 2026.1.16 and Multiwfn 3.8(dev) using the RESP2.sh script from Multiwfn. QM calculations were done using Gaussian 16 Rev. C01.
• See docs/gro-itp-guide.md for custom molecule preparation

Ice Phase Support

QuickIce distinguishes between phase detection and structure generation capabilities:

Phase Detection (12 phases)

The interactive phase diagram can identify 11 ice polymorphs based on temperature and pressure conditions:

Phase	Crystal System	Pressure Range	Temperature Range
Ice Ih	Hexagonal	0-200 MPa	0-273.16K
Ice Ic	Cubic	Low pressure	< 150K
Ice II	Rhombohedral	200-600 MPa	< 250K
Ice III	Tetragonal	200-400 MPa	250-260K
Ice V	Monoclinic	400-600 MPa	250-270K
Ice VI	Tetragonal	600-2000 MPa	250-350K
Ice VII	Cubic	> 2000 MPa	273-355K
Ice VIII	Ordered VII	> 2000 MPa	< 273K
Ice IX	Ordered III	200-400 MPa	< 175K
Ice XI	Ordered Ih	Low pressure	< 72K
Ice XV	Ordered VI	950-2100 MPa	50-100K
Ice X	Symmetric	> 30 GPa	—

Note: Phase boundaries depend on both T and P simultaneously. Ranges above are approximate.

Structure Generation (8 phases)

GenIce2 lattice implementations are available for 8 ice polymorphs:

Phase	GenIce Lattice	Notes
Ice Ih	ice1h	Most common form
Ice Ic	ice1c	Cubic ice
Ice II	ice2	Rhombohedral (no interface support)
Ice III	ice3	Tetragonal
Ice V	ice5	Monoclinic
Ice VI	ice6	Double network
Ice VII	ice7	Double network
Ice VIII	ice8	Ordered Ice VII

Detection-only phases: Ice IX, XI, XV, and X appear in the phase diagram for informational purposes but cannot generate molecular structures. This is a GenIce2 library limitation.

Interface construction: All generatable phases except Ice II work with Tab 2 interface generation. Ice II (rhombohedral) cannot form orthogonal supercells.

Documentation

• GUI Guide — Complete graphical interface documentation
• CLI Reference — Command-line interface for ice generation
• GRO/ITP Guide — Preparing custom molecule files
• Example Scripts — Ready-made CLI examples and workflow scripts
• Ranking Algorithm — How candidates are scored
• Design Principles — Project architecture

Known Issues

Key limitations:

• Ranking uses distance-based energy estimates, not force field calculations
• Some phase boundaries have limited experimental data
• High-pressure phases (> 30 GPa) have larger uncertainties
• Only pure water ice systems supported
• CLI support for v4.5 features (Tabs 3-5) is available via python -m quickice

Dependencies

Package	Purpose
iapws	IAPWS-95 validated water/ice properties
numpy	Numerical operations
scipy	Scientific computing
vtk	3D molecular visualization
PySide6	GUI framework
genice2	Ice structure generation
genice-core	GenIce core algorithms
pytest	Testing framework

References

If you found QuickIce useful, please cite the original publication of GenIce2, and library of ice/water property curves IAPWS.

While QuickIce is mainly a vibe coding project coded by free or open-source LLMs under human supervision, you are also welcomed to cite this repository:

QuickIce GUI, Version [version you use], https://github.com/molmdl/quickice (accessed on [DD MM YYYY])

GenIce2

• Repository: https://github.com/genice-dev/GenIce2
• Paper: "GenIce: Hydrogen-disordered ice structures by combinatorial generation", J. Comput. Chem. 2017
• DOI: https://doi.org/10.1002/jcc.25077

IAPWS R14-08

• Document: "Revised Release on the Pressure along the Melting and Sublimation Curves of Ordinary Water Substance"
• URL: http://www.iapws.org/release/MeltIce.pdf

IAPWS R10-06

• Document: "Revised Release on the Equation of State 2006 for H₂O Ice Ih"
• URL: https://www.iapws.org/release/Ice-2009.html

IAPWS-95

• "Revised Release on the IAPWS Formulation 1995 for the Thermodynamic Properties of Ordinary Water Substance for General and Scientific Use"
• URL: https://www.iapws.org/relguide/IAPWS-95.html

Journaux et al. (2019, 2020)

• Journaux, B. et al. (2019). J. Geophys. Res.: Planets, 124. DOI: 10.1029/2019JE006176
• Journaux, B. et al. (2020). Space Sci. Rev., 216, 7. DOI: 10.1007/s11214-019-0634-7

Petrenko & Whitworth (1999)

• Petrenko, V. F. & Whitworth, R. W. (1999). Physics of Ice. Oxford University Press. ISBN: 978-0198518945

CODATA 2017

• Tiesinga, E. et al. (2021). Rev. Mod. Phys., 93(2), 025010. DOI: 10.1103/RevModPhys.93.025010

spglib

• Repository: https://github.com/atztogo/spglib
• Paper: "Spglib: a software library for crystal symmetry search", Sci. Technol. Adv. Mater., Meth. 4, 2384822 (2024)
• DOI: https://doi.org/10.1080/27660400.2024.2384822

Multiwfn

• Tian Lu, Feiwu Chen, Multiwfn: A Multifunctional Wavefunction Analyzer, J. Comput. Chem. 33, 580-592 (2012)
• DOI: 10.1002/jcc.22885
• Tian Lu, A comprehensive electron wavefunction analysis toolbox for chemists, Multiwfn, J. Chem. Phys., 161, 082503 (2024)
• DOI: 10.1063/5.0216272

Sobtop

• Tian Lu, Sobtop, Version 2026.1.16, http://sobereva.com/soft/Sobtop (accessed on 15 Apr 2026)

GAFF / GAFF2

• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. DOI: https://doi.org/10.1002/jcc.20035
• He, X., Man, V. H., Yang, Y., Wang, L.-P., & Merz, K. M. (2020). A fast and high-quality charge model for molecular mechanical force fields. Journal of Chemical Information and Modeling, 60(5), 247–257. DOI: https://doi.org/10.1021/acs.jcim.9b01131

Gaussian 16 Rev. C01

• Gaussian 16, Revision C.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, R. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. P. Rendell, J. C. Burant, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016.

Madrid2019 Ion Parameters

• Zeron, I. M., Abascal, J. L. F., & Vega, C. (2019). A force field of Li+, Na+, K+, Mg2+, Ca2+, Cl−, and SO42− in aqueous solution based on the TIP4P/2005 water model and scaled charges for the ions. Journal of Chemical Physics, 151, 134504.
• DOI: https://doi.org/10.1063/1.5121392

Madrid2019 / TIP4P-ICE Compatibility

• The Madrid2019 ion model (±0.85e charges) was parameterized for TIP4P/2005 water. QuickIce uses these parameters with TIP4P-ICE water, which is common practice but technically a force field combination.
• Zeron et al. (2019). J. Chem. Phys. 151, 134504. DOI: 10.1063/1.5121392

Testing

# Run test suite
pytest

# Verbose output
pytest -v

# Specific test module
pytest tests/ -k solute -q

Project Structure

quickice/
├── quickice.py          # Backward-compat entry wrapper
├── quickice/__main__.py # Unified entry point (python -m quickice)
├── quickice/entry.py    # Entry router (CLI/GUI routing)
├── quickice/            # Main package
│   ├── cli/             # Command-line interface
│   ├── gui/             # Graphical User Interface
│   ├── phase_mapping/   # T,P → ice polymorph lookup
│   ├── structure_generation/  # GenIce2 integration
│   ├── ranking/         # Candidate scoring
│   ├── output/          # PDB/GROMACS export
│   └── data/            # Bundled force field files
├── docs/                # Documentation
├── sample_output/       # CLI output examples
├── environment.yml      # Conda environment
└── setup.sh             # Environment setup script

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QuickIce v4.5 — Solute & Custom Molecule Insertion Last updated: 2026-06-15