Choose Task Type

Select the type of system you want to build. Grayed-out cards are planned for future releases.

Tasks expire after 8 hours of inactivity.

Membrane builder under active development

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.

yanghaochen2021@sibcb.ac.cn

Simulation Parameters

Six-stage equilibration with decaying restraints, followed by production. Click any stage to expand and tune.

Upload Structure File

⇧

Drag & drop a PDB or CIF file here, or

Accepts PDB (.pdb/.ent), mmCIF (.cif/.mmcif), and gzip-compressed variants

Martini 3 Model

Verify the bundled Martini 3.0.0 parameters, 2025 lipidome v2, regular water, and pinned mapping/build tools.

Immutable model: Martini 3 with regular W water and NA/CL ions. Force-field checksums and exact tool versions are validated for every task.

Protein Mapping

Map the uploaded standard protein with pinned Martinize2. This step is skipped for a protein-free bilayer.

H/B/E/G/I/T/S/C; required only in manual mode

Protein Orientation in Membrane

Determine how the mapped Martini protein is positioned in the lipid bilayer — insertion depth and tilt angle.

PPM-like — Wimley-White/CG hydrophobic-segment scan
Z-offset— nm
Tilt refinement—°
DescriptionLocal 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.

Membrane Position Preview — grey planes show membrane

CG Environment

Build the Martini 3 environment from explicit molecular composition.

The initial periodic X/Y area is derived automatically from the exact count and a conservative composition-weighted construction area; NPT equilibration relaxes the area.

Bilayer (same composition in both leaflets)

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.

CG Solvation

Set the solvent padding and add regular Martini water. Target bulk salt is added in the next Ions step.

The membrane X/Y area remains fixed by the bilayer composition.

Ions & Final CG System

Add neutralizing ions and target bulk salt, then enforce charge, box, solvent, and membrane-quality checks on the exact export coordinates.

Force Field Selection

Choose force fields for each component type before building the system. This choice affects hydrogen addition, water model compatibility, and topology generation.

Amber14SB + GAFF2 is the project default for proteins with organic small molecules. The new native GROMACS Amber14SB port is still validation-pending; production systems require topology and energy QA.
Only parameter families compatible with the selected protein force field and current Step 5 lipids are enabled.
For GAFF2, set the solution pH and review each molecule's suggested integer net charge. For CHARMM, use the local builder with an explicit molecular state, or upload the matched MOL2 and STR from CGenFF/ParamChem.
Only models bundled with the selected effective force field are available. This choice is locked for Step 6 and final topology export.

Structure Processing

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.

Protein Orientation in Membrane

Determine how the protein is positioned in the lipid bilayer — insertion depth and tilt angle.

Z-offset— nm
TM bundle tilt—°
DescriptionWimley-White whole-residue transfer free energy minimization.

ⓘ If the orientation appears incorrect, try a different auto algorithm or switch to Manual Adjustment.

Membrane Position Preview — grey planes show membrane

Membrane Builder

Minimum supported construction size: 64 per leaflet. Maximum: 5000. Larger systems reduce finite-size effects, but stability must be assessed by equilibration.

Bilayer (same composition both leaflets)

Membrane plane (grey) shows the bilayer extent. Adjust Padding to resize.

Solvation

Selected and compatibility-checked in Step 2. Return to Force Field Selection to change it.
Box XY is fixed by Membrane step; this padding only extends the Z (vertical) direction.
Fraction of vdW radius sum used for overlap cutoff
Solvation box — XY from membrane, Z from padding

Ions

Add salt ions and neutralize system charge. Select one or more cation / anion species.

Cations (+)

Anions (−)

All methods replace complete waters at oxygen coordinates. Seeded random replacement is the validated default. Experimental modes optimize heuristic formal-charge scores; they are not equilibrium ion sampling and should not be interpreted as a physical ion distribution.

Neutralizing Ions

for neutralizing negative solute charge
for neutralizing positive solute charge

Complete Simulation System — exact coordinates saved by Ion Check

Waters are shown in blue; ions are shown as large spheres.
Run Check Ion Counts to generate the final system preview.