; NVT production (analysis-quality) integrator = md dt = 0.002 nsteps = 5000000 ; set time (e.g., 10 ns) constraints = h-bonds constraint-algorithm = lincs lincs_iter = 1 lincs_order = 4 cutoff-scheme = Verlet nstlist = 20 ns_type = grid rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 DispCorr = EnerPres coulombtype = PME pme_order = 4 fourierspacing = 0.12 ; Proper production thermostat tcoupl = Nose-Hoover tc-grps = System tau_t = 1.0 ref_t = 298 pcoupl = no ; Continue from relax stage continuation = yes nstcomm = 100 comm-mode = linear comm-grps = System ; Output: good for H-bond lifetimes + MSM nstenergy = 2500 ; 2 ps nstlog = 2500 nstxout = 0 nstvout = 0 nstfout = 0 nstxout-compressed = 500 ; 5 ps (set to 500 for 1 ps if you can) compressed-x-precision = 500 pbc = xyz ; ---------- Electric field placeholders ---------- ; E_z = 0.5 ; (oscillating field syntax depends on GROMACS version)