title = DMSO NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 2000 dt = 0.001 ; Output control nstxout = 0 nstvout = 0 nstfout = 0 nstxout-compressed = 500 ; write .xtc every 200 steps nstenergy = 500 ; keep energies nstlog = 500 ; keep log ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) rlist = 1.2 DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = fluid SUR ;UNL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xy ; 3-D PBC periodic-molecules =yes ewald-geometry = 3dc nwall = 2 ; wall at z=0 and z=z-box wall-type = 12-6 ; direct 12-6 LJ as fn of distance from wall wall-ewald-zfac = 3 ; Extra empty space for slab geometry calculation (reducing coulomb interaction) wall-atomtype = MA MA ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution ;gen_temp = 300 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed nstcomm = 1 comm-mode = Linear comm-grps = System ;electric-field-z = 0.4 0 0 0