MACS Research Documentation

MDP Consistency Report

Project: MACS
Document type: Technical Documentation
Year: 2026
Research status: Computational Discovery

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.

Table 1 — Audited production MD parameters
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.