; Run control integrator = md-vv tinit = 0 dt = 0.002 nsteps = 1000000000 ; 2000 ns comm-mode = Linear nstcomm = 1 ; Output control nstlog = 1000 nstcalcenergy = 1 nstenergy = 1000 nstxout-compressed = 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 ; Electrostatics cutoff-scheme = verlet coulombtype = PME coulomb-modifier = Potential-shift-Verlet rcoulomb-switch = 0.89 rcoulomb = 0.9 ; van der Waals vdw-type = Cut-off vdw-modifier = Potential-switch rvdw-switch = 0.85 rvdw = 0.9 ; Apply long-range dispersion corrections for Energy and Pressure DispCorr = AllEnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 ; EWALD/PME/PPPM parameters fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 ; Temperature coupling tcoupl = v-rescale nsttcouple = 1 tc_grps = System tau_t = 0.5 ref_t = 310.15 ; Pressure coupling is on for NPT pcoupl = Parrinello-Rahman ; no pressure for NVT equilibration pcoupltype = isotropic tau-p = 5.0 ref-p = 1.0 ; bar compressibility = 4.5e-5 ; For water at 1 atm and 300 K the compressibiilty is 4.5e-5 bar^(-1) ; refcoord_scaling should do nothing since there are no position restraints. gen_vel = no ; gen-temp = 310.15 ; gen-seed = 6722267; need to randomize the seed each time. ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 lincs-iter = 2