Upload a protein complex, assign receptor and ligand chains, run MD + MM/PBSA on Modal, and inspect energy results and trajectory artifacts in one workspace.

The workspace turns a reviewed soluble protein complex into a persisted typed workflow with topology, solvent, ions, equilibration, production dynamics, and an auditable MM/PBSA estimate.

Structure file

.pdb or .ent, no larger than 20 MiB. Standard protein ATOM records are supported; unparameterized non-water HETATM records are rejected.

Partner chains

Required, non-overlapping receptor and ligand chain-ID groups used for the MM/PBSA split.

Protocol

Validation (20 ps), preliminary screening (1 ns), or production estimate (10 ns), plus temperature (273–330 K).

Advanced mode

An optional analysis-start time can override RMSD-window detection; raw gmx commands remain separate expert diagnostics.

Energy results

Total, van der Waals, electrostatic, polar-solvation, and non-polar-solvation means and frame-wise standard deviations.

MD artifacts

Cα RMSD XVG/CSV, stability JSON, selected-window XTC, production TPR, representative/residue-energy PDBs, energy/residue CSVs, and workflow log.

Persisted workspace

Stage progress, chain assignments, protocol, files, interpretation limits, and representative structure reopen from history.

1. 1. Open Binding Energy · MD and drop or browse to a reviewed protein-complex PDB/ENT file

   Open Binding Energy · MD and drop or browse to a reviewed protein-complex PDB/ENT file.

2. 2. Confirm detected chains, then assign non-overlapping receptor and ligand chain groups

   Confirm detected chains, then assign non-overlapping receptor and ligand chain groups.

3. 3. Choose the validation, screening, or production preset and review temperature and output contract

   Choose the validation, screening, or production preset and review temperature and output contract.

4. 4. Follow the selected task below the history strip until it reaches a terminal state

   Follow the selected task below the history strip until it reaches a terminal state.

5. 5. Open Overview to verify the RMSD trace and selected energy window before reading MM/PBSA and residue contributions; use Files for the complete audit artifacts

   Open Overview to verify the RMSD trace and selected energy window before reading MM/PBSA and residue contributions; use Files for the complete audit artifacts.

6. 6. Use inputs again only when you intentionally want to prepare a new run from a saved task

   Use inputs again only when you intentionally want to prepare a new run from a saved task.

• POST /api/v1/gromacs/binding-energy/jobs validates and persists the typed request before background execution starts.
• Modal calls gromacs-2026-3/binding_energy with GROMACS 2026.3 CUDA and g_mmpbsa 3.0.14; stage progress is persisted separately.
• The workflow uses Amber99SB-ILDN/TIP3P, 0.15 M ions, minimization, NVT/NPT, production MD, PBC correction, backbone-fitted Cα RMSD, an audited analysis window, and MM/PBSA residue decomposition.
• Advanced raw commands still use POST /api/v1/gromacs/jobs and retain strict shell/operator and file-count limits.

• Missing partner chains, overlapping groups, non-standard residues, or unparameterized HETATM records are rejected before compute.
• Validation and screening presets are not decision-grade; compare production runs only under a matched protocol and use independent replicas.
• An RMSD plateau is a coordinate-stability diagnostic, not proof of thermodynamic convergence; a no-plateau run is labelled diagnostic rather than silently promoted.
• A cold Modal worker can remain running longer than a warm invocation; leaving the page does not cancel it.
• Do not convert MM/PBSA values directly to Kd/IC50 or treat one trajectory as proof of binding, specificity, or mechanism.