Dear GMX Users I want to equilibrate my system in NVT from 0 to 300 K then in NPT (300K). Is my mdp file in NVT equilibration is correct?
define = -DPOSRES ; Run control integrator = md dt = 0.002 ; ps ! nsteps = 50000 ; total 100.0 ps. ; Output control nstxout = 500 ; collect data every 1.0 ps nstvout = 500 ; collect data every 1.0 ps nstfout = 0 nstlog = 500 ; collect data every 1.0 ps nstenergy = 500 ; collect data every 1.0 ps nstxtcout = 500 xtc-precision = 500 nstcalcenergy = 10 energygrps = DNA_LIG Water_counterions ; Neighbor searching and short-range nonbonded interactions nstlist = 5 ns_type = grid pbc = xyz rlist = 1.0 ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; van der Waals vdw-type = cut-off rvdw = 1.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 4 ; Temperature coupling tcoupl = V-rescale tc_grps = DNA_LIG Water_counterions tau_t = 0.1 0.1 ref_t = 300 300 ; SIMULATED ANNEALING annealing = single single annealing_npoints = 7 7 annealing_time = 0 15 30 45 60 80 100 0 15 30 45 60 80 100 annealing_temp = 0 50 100 150 200 250 300 0 50 100 150 200 250 300 ; Pressure coupling is on for NPT pcoupl = no ; Dispersion correction DispCorr = EnerPres ; generate velocities gen_vel = yes gen_temp = 300 gen_seed = -1 ; options for bonds continuation = no constraints = all-bonds constraint-algorithm = lincs ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 lincs_iter = 1 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.