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

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 modelElectrostatics:- 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 ProtocolsS2.3.1 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 EquilibrationDuration: 100 nsEnsemble: 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 independentIntegration:- Time step: 20 fs (0.020 ps, standard for MARTINI)- Neighbor list update: every 10 stepsPosition restraints:- Protein backbone: 1000 kJ mol⁻¹ nm⁻² (first 50 ns)- Released gradually over 50-100 nsOutput:- Coordinates: every 1 ns- Energies: every 100 ps S2.3.3 Production RunDuration: 10 μs total for all systemsEnsemble: NPTTemperature 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 independentIntegration:- 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 savedPeriodic boundary conditions: xyz (all dimensions)Neighbor searching:- Method: Verlet cutoff scheme- Cutoff: 1.4 nm- Update frequency: automatically determined by GROMACS