Get the Structure Right Before You Compute
Every molecule of a study in one table, checks that catch mistakes early, and a preparation grid that never pretends.
Structures
A study tab, always shown, with one sub-tab per kind of structure.
Molecules Live
Name, formula, charge, multiplicity, atoms, Library link, check state and the computations using each molecule. Select one to see it in 3D. Add or edit in the Molecule Editor, export .xyz, save to the Library.
Biomolecules Planned
Proteins, nucleic acids and ligand complexes from structure files, with residue templates from published data.
Crystals, Surfaces, Polymers Planned
Unit cells, slabs and interfaces, and repeat units, arriving with Materials Science.
System Preparation, Step by Step
One grid: molecules down the side, the ordered preparation steps across the top. Each cell is Done, Problems, Not run, Awaiting data or Planned.
| Step | Status | What It Does and What It Needs |
|---|---|---|
| 1 Clean Up | Partial | Geometry relaxation with our MMFF94 minimiser. The engine is ready; the app step still shows Awaiting data while it is switched over. |
| 2 Protonation States and Tautomers | Planned | Needs a published pKa method rebuilt and validated against published pKa data. |
| 3 Conformer Search | Partial | MMFF94 conformer search runs in the engine; the app step is not wired yet. |
| 4 Solvent and Ions | Planned | Explicit solvent box and counter-ions, arriving with Molecular Dynamics. |
| 5 Atom Typing and Parameters | Partial | The engine reads and types the structure with MMFF94; the app step is being switched over from Awaiting data. |
| 6 Structure Checks | Live | Charge and multiplicity parity, close contacts under 0.5 Å, isolated atoms and over-bonded hydrogens, then the engine reads the structure. Covalent radii are flagged Unverified until sourced. |
Rules That Keep It Honest
- Running a step never changes a stored structure
- A planned step explains what it waits for instead of showing a fake button
- Force fields and basis sets stay method settings in each domain's Setup
- Every rule cites its original paper or textbook; unchecked data is labelled Unverified
Preparation Questions
Does running the checks change my structures?
Why does Clean Up say Awaiting data?
Can I bring proteins or crystals?
Where are force fields and basis sets chosen?
Run Your Next Molecule Through AiMolSim
Connect your own server once, then let your team queue computations from the browser.