v1.0.2
Select an available workflow to start building. Planned workflows are listed separately below.
Tasks expire 24 hours after creation. Viewing or downloading does not extend this time.
Some lipids are temporarily unavailable for certain force fields. Due to limited computing capacity, the pre-equilibration queue for the full lipid library is still in progress. Each lipid will become available for selection as soon as its pre-equilibration calculations are complete. Thank you for your patience and understanding.
The membrane builder is being improved further. Please note the backend version shown in the page header when reporting anything, and get in touch if you run into a problem.
Approximate locations · 5° grid
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Six-stage equilibration with decaying restraints, followed by production. Click any stage to expand and tune.
Reaction-field electrostatics and Martini 3 cutoffs are fixed to prevent incompatible parameter combinations.
V-rescale thermostat; velocities are generated only for the first enabled dynamics stage.
Pressure geometry is automatically semi-isotropic for bilayers and isotropic for solution systems.
CPU threads must be exactly divisible by ranks. GPU IDs are passed only to short-ranged non-bonded work.
Drag & drop a PDB or CIF file here, or
Accepts PDB (.pdb/.ent), mmCIF (.cif/.mmcif), and gzip-compressed variants
Verify the bundled Martini 3.0.0 parameters, 2025 lipidome v2, regular water, and pinned mapping/build tools.
Map the uploaded standard protein with pinned Martinize2. This step is skipped for a protein-free bilayer.
Determine how the mapped Martini protein is positioned in the lipid bilayer — insertion depth and tilt angle.
| Z-offset | — nm |
| Tilt refinement | —° |
| Description | Local PPM-like transfer-energy minimization over mapped Martini backbone beads. Review the result because this is not the external OPM/PPM server. |
ⓘ If the orientation appears incorrect, switch to Manual Adjustment.
Build the Martini 3 environment from explicit molecular composition.
This viewer shows the dry COBY construction geometry with topology-defined Martini bead connections. It is not an energy-minimized or equilibrated membrane. Use the exported minimization, NVT, and semi-isotropic NPT stages before interpreting bilayer structure or properties.
Set the solvent padding and add regular Martini water. Target bulk salt is added in the next Ions step.
Add neutralizing ions and target bulk salt, then enforce charge, box, solvent, and membrane-quality checks on the exact export coordinates.
After this Check, continue to Final Structure Review to inspect and confirm the saved system.
Choose force fields for each component type before building the system. This choice affects hydrogen addition, water model compatibility, and topology generation.
Assign protonation states, cap termini, and apply post-translational modifications — per chain.
Upload a PDB to begin.
Side-chain pKa estimation supports pH 1.0–13.0. Free termini are built as the canonical NH₃⁺/COO⁻ templates, whose bounds follow the model pKa values: both states are dominant between pH 4.45 and 7.05, remain the majority species out to pH 3.50–8.00 where the build continues with a warning stating the actual population, and beyond that the build stops because a cap is then the better model. Cap a chain with ACE/FOR and NME in the Termini tab when it is a truncated construct; a full-length protein normally keeps its free charged termini.
Determine how the protein is positioned in the lipid bilayer — insertion depth and tilt angle.
| Z-offset | — nm |
| TM bundle tilt | —° |
| Description | Wimley-White whole-residue transfer free energy minimization. |
ⓘ If the orientation appears incorrect, try a different auto algorithm or switch to Manual Adjustment.
Select a composition and build the membrane to inspect its coordinates. The initial view is a geometric preview.
Membrane plane (grey) shows the bilayer extent. Adjust Padding to resize.| Box dimensions | — |
| Box volume | — nm³ |
| Water molecules | — |
| Water model | — |
Add salt ions and neutralize system charge. Select one or more cation / anion species.
| Ion | Charge | Salt pairs | Neutralizing | Total count | Effective conc (M) |
|---|
Inspect the exact checked system and its components before choosing simulation parameters.
The complete checked structure will appear here.
Wait for the complete structure to render before confirming.