MDP Consistency Report
This report verifies the consistency of Molecular Dynamics parameter (MDP) settings used across the MACS simulation systems. Key production parameters were audited to ensure fair comparison between the pH 6.8 and pH 7.4 conditions.
Production MD Parameters (300 ns)
The audited production parameters matched between the pH 6.8 and pH 7.4 systems for the compared settings.
| Parameter Group | Setting (pH 6.8 & pH 7.4) |
|---|---|
| Run Control | integrator = md dt = 0.002 nsteps = 150000000 (300 ns) continuation = yes |
| Constraints | constraint_algorithm = lincs constraints = h-bonds |
| Non-bonded & Electrostatics | cutoff-scheme = Verlet coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 |
| Temperature Coupling | tcoupl = V-rescale tc-grps = Protein Non-Protein ref_t = 310 tau_t = 0.1 |
| Pressure Coupling | pcoupl = C-rescale pcoupltype = isotropic ref_p = 1.0 tau_p = 5.0 compressibility = 4.5e-5 |
Verification Conclusion
No material differences were identified among the audited production-MD settings used for the comparative trajectories. Both conditions used the same core production setup, including V-rescale temperature coupling, C-rescale pressure coupling, and PME electrostatics, and continued from their preceding NPT equilibration steps.
Any transient differences observed in intermediate mdout.mdp files (e.g., minimization versus MD steps) strictly correspond to the equilibration sequence and not the final 300 ns comparative trajectories.