| define = | |
| ; Integrator stuff | |
| integrator = md ; steep or md | |
| dt = 0.002 | |
| nsteps = 250000000 ; -1 no maximum | |
| init-step = 0 ; | |
| continuation = no | |
| ; neighbour search | |
| cutoff-scheme = verlet ; the other is bad | |
| nst-list = 10 ;frequency of update of neighbours, with verlet-buf-tol its a minimum | |
| verlet-buffer-tolerance = 0.005 ; kj/mol/ps might need to put -1. | |
| ns-type = grid | |
| ; Pbc | |
| pbc = xyz ; xyz or xy | |
| ; Vdw | |
| rvdw = 1.0 | |
| vdwtype = cut-off ; PME or User to look for table /user | |
| DispCorr = EnerPres ; corrections to energy and pressure or No | |
| ;Electrostatic | |
| coulombtype = PME ; User if look for table | |
| rcoulomb = 1.0 | |
| pme-order = 4 | |
| fourierspacing = 0.1 | |
| ewald-rtol = 1.e-5 ; splitting between real and reciprocal | |
| ewald-geometry = 3d ; 3d or 3dc | |
| IMD-group = non-Water | |
| ; T and P | |
| tcoupl = v-rescale ; none, nose-hoover, v-rescale | |
| nsttcouple = 10 ; 10 if not used | |
| tc-grps = OCB MOL Water_and_ions | |
| tau-t = 0.1 0.1 0.1 ; ps | |
| ref-t = 300 300 300 ; K | |
| pcoupl = no ; | |
| pcoupltype = isotropic ; | |
| compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 | |
| refcoord-scaling = com | |
| tau-p = 5.0 ; ps | |
| ref-p = 1.0 ; bar | |
| ; Constraints | |
| constraints = all-bonds ; constraints distances | |
| constraint-algorithm = LINCS ; or SHAKE | |
| lincs_iter = 1 | |
| lincs_order = 4 | |
| ;Generate velocities | |
| gen_vel = yes ; assign velocities from Maxwell distribution | |
| gen_temp = 300 ; temperature for Maxwell distribution | |
| gen_seed = -1 ; generate a random seed | |
| ; OUTPUT | |
| ; Output control | |
| nstenergy = 1000 ; save energies | |
| nstlog = 1000 ; update log file every | |
| nstxout = 500 ; save coordinates every 1.0 ps | |
| ; nstxout-compressed replaces nstxtcout | |
| ; COM removal . There are more options like removing from groups or the frequency | |
| comm-mode = linear ; linear, angular (removes linear and angular motion) or none | |
| nstcomm = 100 ; frequency of removal of com motion | |
| nstcalcenergy = 500 | |