; ; Input file ; title = imine+DNA ; a string cpp = /lib/cpp ; c-preprocessor ; ; RUN CONTROL ; integrator = md dt = 0.001 nsteps = 300000 ; number of steps init_step = 0 ;if there is need to restart, see tpbconv program comm_mode = angular ; removal of translational and rotational CM motion nstcomm = 10 ;frequency of the removal comm_grps = IMI DNA solvent ;group(s) for CM motion removal, default is all system ; ; ENERGY MIN ; ;emtol = 100 ;(kJ/mol x nm) ;emstep = 0.01 ;nstcgsteep = 1000 ;nbfgscorr = 10 ; ; OUTPUT CONTROL ; nstcheckpoint = 1000 ; checkpointing helps you continue after crashes ;nstxtcout = 0 ; output frequency and precisionfor xtc file ;xtc-precision = 1000 nstxout = 1000 ; write coords nstvout = 1000 ;nstfout nstlog = 1000 ; print to logfile nstenergy = 1000 ; print energies energygrps = IMI DNA solvent ; ; NEIGHBOR SEARCHING ; nstlist = 15 ; update pairlist ns_type = grid ; pairlist method pbc = xyz rlist = 1.2 ; cut-off for ns ; ; ELECTROSTATIC AND VDWAALS ; coulombtype = PME ;rcoulomb_switch = 0 rcoulomb = 1.2 ; cut-off for coulomb epsilon_r = 1 ;vdwtype ;rvdw_switch = 0 rvdw = 1.2 ; cut-off for vdw DispCorr = EnerPres ; Apply long range dispersion corrections for Energy and Pressure fourierspacing = 0.12 fourier_nx = 64 fourier_ny = 60 fourier_nz = 66 ewald_rtol = 1e-5 pme_order = 4 optimize_fft = yes ; ; T COUPLING ; tcoupl = Nose-Hoover tc_grps = IMI DNA solvent ref_t = 310. 310. 310. tau_t = 2.0 2.0 1.0 ; ; P COUPLING ; pcoupl = Parrinello-Rahman compressibility = 4.5e-5 tau_p = 1.0 ref_p = 1.0 pcoupltype = isotropic ; ; SIMULATED ANNEALING ; ;annealing ;annealing_npoints ;annealing_time ;annealing_temp ; ; VEL GEN ;gen_vel = yes ;gen_temp = 310 ;gen_seed = 173529 ; ; BONDS ; constraints = h-bonds constraint_algorithm = lincs lincs_order = 4 ; ; FREE ENERGY PERTURBATION ; ;free_energy ;init_lambda = 0 ;delta_lambda = 0 ;sc_alpha = 0 ;sc_sigma = 0.3 ; ; NON EQ MD ; ;acc_grps ;accelerate = 0 ;freezegrps ;freezedim ;cos_acceleration = 0