;define = ; Running integrator = md ;nsteps = 50000000 ; 100 ns nsteps = 5000 dt = 0.002 ; Output options ; =================================================================== comm_mode = linear; Linear: Remove center of mass translation comm_grps = system; group(s) for center of mass motion removal, default is the whole system nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 100 ; frequency to write coordinates to xtc trajectory nstlog = 0 nstenergy = 0 ; Constraints ; =================================================================== constraints = hbonds; standard spc/e: 3 lengths -> also angle fixed ;constraint-algorithm = SHAKE; compare to LAMMPS ; neighbor searching ; =================================================================== ;cutoff-scheme = verlet; use new Verlet cut-off scheme ns_type = grid nstlist = 10; no influence on accurracy? pbc = xyz rcoulomb = 0.9; distance for the Coulomb cut-off rlist = 0.9; cut-off distance for the short-range neighbor list - with Verlet ignored! rvdw = 0.9; distance for the LJ or Buckingham cut-off ; Electrostatics ; =================================================================== coulombtype = pme fourierspacing = 0.1; This should give an accuracy of about 2-3*10^-4 pme-order = 4; ; VdW ; =================================================================== vdw-type = Cut-off ;vdw-modifier = Potential-shift ;vdw-modifier = None ;DispCorr = EnerPres ; do dispersion correction DispCorr = no ; group(s) to write to energy file energygrps = SOL tcoupl = v-rescale tc_grps = SOL tau_t = .5 ref_t = 300 gen-vel = no