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 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