DOI: 10.5281/zenodo.18382504
title: Trajectory for MD simulation on Notch TM-JM sequence in ordered membrane

description: Trajectory for MD simulation on Notch TM-JM sequence in ordered membrane.

Protein:

- Source: PDB entry (Notch transmembrane domain structure)

- Residues: 1721-1771 (transmembrane domain)

- Number of copies: 4

- Chains labeled A, B, C, D

- Conversion: martinize2 version 2.6 with elastic network constraints

 

Membrane:

- Box dimensions: 40 × 40 × 10 nm³

- Total lipid molecules: ~5300

 

Upper leaflet (analyzed):

- DIPC: 33 mol%

- CHOL: 33 mol%

- DPSM (sphingomyelin): 33 mol%

 

Lower leaflet (not analyzed):



DIPC: 33 mol%

CHOL: 33 mol%

DIPS (dilinoleoyl phosphatidylserine): 33 mol%


 

Force field: MARTINI 2.2 with MARTINI protein model

Electrostatics:

- Method: Reaction-field

- Cutoff: 1.2 nm

- Relative dielectric constant (εᵣ): 15 (MARTINI standard)

 

Van der Waals:

- Method: Shifted potential

- Cutoff: 1.2 nm

- Switch: 1.0 nm (shifted to zero at cutoff)

 

Constraints:

- Protein elastic network: Enabled (maintains secondary structure)

- Cutoff: 0.9 nm (backbone beads)

- Force constant: 500 kJ mol⁻¹ nm⁻²

- Bond constraints: None (MARTINI uses harmonic bonds)

 

Lipid parameters:

- DIPC: MARTINI lipid type "C1A" headgroup, "C1" tail beads

- DOPS/DIPS: MARTINI lipid type "C1A" headgroup with charge

- CHOL: MARTINI cholesterol model (4 beads)

- DPSM: MARTINI sphingomyelin model

 

S2.3 Simulation Protocols

S2.3.1 Energy Minimization

- Algorithm: Steepest descent

- Convergence criterion: Maximum force < 10 kJ mol⁻¹ nm⁻¹

- Typical steps: 5,000-10,000

- Purpose: Remove steric clashes from initial structure

 

S2.3.2 Equilibration

Duration: 100 ns

Ensemble: NPT (constant number, pressure, temperature)

Temperature control:

- Target: 298 K

- Thermostat: Velocity-rescale (v-rescale, modified Berendsen)

- Time constant: 1.0 ps

- Coupling groups: Protein, lipids, solvent (separately coupled)

Pressure control:

- Target: 1 bar

- Barostat: Semi-isotropic Berendsen

- Time constant: 5.0 ps

- Compressibility: 3 × 10⁻⁴ bar⁻¹

- Semi-isotropic: xy plane coupled, z independent

Integration:

- Time step: 20 fs (0.020 ps, standard for MARTINI)

- Neighbor list update: every 10 steps

Position restraints:

- Protein backbone: 1000 kJ mol⁻¹ nm⁻² (first 50 ns)

- Released gradually over 50-100 ns

Output:

- Coordinates: every 1 ns

- Energies: every 100 ps

 

S2.3.3 Production Run

Duration: 10 μs total for all systems

Ensemble: NPT

Temperature control:

- Same as equilibration (298 K, v-rescale, τ = 1.0 ps)

Pressure control:

- Target: 1 bar

- Barostat: Parrinello-Rahman (more accurate than Berendsen for production)

- Time constant: 12.0 ps (longer than equilibration to reduce fluctuations)

- Compressibility: 3 × 10⁻⁴ bar⁻¹

- Semi-isotropic: xy plane coupled, z independent

Integration:

- Time step: 20 fs

- Neighbor list update: every 10 steps (with Verlet scheme)

Output frequencies:

- Coordinates: every 100 ps (5000 steps)

- Energies: every 100 ps

- Velocities: not saved (to reduce file size)

- Forces: not saved

Periodic boundary conditions: xyz (all dimensions)

Neighbor searching:

- Method: Verlet cutoff scheme

- Cutoff: 1.4 nm

- Update frequency: automatically determined by GROMACS