Preview release under active development.
Instabilities and breaking changes may occur.
Validate results before using them in production simulations.
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Membrane builds
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Atoms assembled
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Unique users
12
Lipid types
Upper leaflet
Lower leaflet
Surface peptide (optional)
No file selected
Solvation
No anionic lipids in this composition. Counter-ions at headgroup are not required.
Parameters
Simplified model. Preset compositions are based on published averages and use a reduced set of generic phospholipid species as proxies for the acyl chain diversity found in native membranes. The following are not represented: post-translational lipid modifications (glycosylation, acylation, methylation), asymmetric leaflet distributions, membrane proteins, and LPS in Gram-negative bacteria. Species-specific simplifications: B. subtilis omits glycolipids (~30% of native total lipid) and L-PG; M. tuberculosis uses SAPI as a proxy for phosphatidylinositol mannosides (PIM2/PIM6); H. pylori approximates cholesterol glucosides as free CHOL; S. cerevisiae uses CHOL as a proxy for ergosterol. These presets are starting points for simulation setup and should be validated against organism- and condition-specific experimental data before drawing conclusions.
Assembly notes and recommendations
Important notice
BILBO is under active development and is being used and tested by research groups in theoretical chemistry and biophysics. The membrane builder, topology generator, and GROMACS MD package export are functional, but edge cases and unsupported lipid combinations may still produce unexpected results. Contributions and feedback are welcome. Please report issues via the or at github.com/madsondeluna/bilbo/issues.
Bilayer gap is a buffer, not experimental
The inter-leaflet half-gap (default 2.5 A per leaflet) prevents tail overlap in the template-tiled structure. It does not represent measured bilayer thickness. Adjust and re-minimize as needed.
Asymmetric bilayers
When upper and lower leaflets differ in composition, check that the lipid area per molecule is compatible between leaflets. A large area mismatch produces curvature stress that persists even after minimization.
Lipid template names
Template PDB filenames must match the lipid residue name (case-insensitive). The preset lipids (POPE, POPG, POPC, DPPC, DPPE, DPPG, DPPS, POPS, CHOL, BSM, SAPI, CL) are supported directly. For other lipids, upload a single-residue PDB via the custom template field or the CLI (
bilbo membrane build --templates-dir). CHARMM-GUI PDB files with co-packaged water are handled automatically.
Inter-residue clashes are expected
Template-tiled membranes place lipids on a regular grid from single-molecule PDB templates. Short inter-residue distances (clashes) are normal in the initial structure and do not indicate a build error. Run energy minimization (EM) before NVT equilibration; the bundled
gmx.sh handles this automatically.
MD package: what is included
The MD package ZIP contains a complete, self-contained GROMACS run directory:
system.pdb, topol.top, MDP files (EM, NVT, NPT, production), an automated run script (gmx.sh), and the full CHARMM36 force field (MacKerell lab, Feb 2026 release with CGenFF 5.0). GROMACS 2021 or newer must be installed; no additional downloads are required. Simulation parameters (trajectory length, temperature, equilibration time, output frequency) are configurable before download.
Atom count limit
PDB serial numbers wrap at 99,999 atoms; residue numbers wrap at 9,999. BILBO handles this automatically, but downstream tools that rely on unique serial numbers should use the GRO file instead.
Where BILBO is used
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