Hi all the users, When I use the command "mdrun"to simulate the CG DNA model, I found that all the files are output expect the trajectory file. I will list some parts of my mdp.file
; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit = 0.0 dt = 0.03 nsteps = 1000000 ; number of steps for center of mass motion removal = nstcomm = 1 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file = nstxtcout = 1000 xtc_precision = 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = plan1 NA CL W ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.2 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 20 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.15 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.3 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order = 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = tc-grps = plan1 NA CL W ; Time constant (ps) and reference temperature (K) = tau_t = 1.0 1.0 1.0 1.0 ref_t = 300 300 300 300 ; Pressure coupling = Pcoupl = no Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 1.0 compressibility = 1e-5 ref_p = 1.0 ; SIMULATED ANNEALING CONTROL = annealing = no ; Time at which temperature should be zero (ps) = zero_temp_time = 0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Relative tolerance of shake = shake_tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 ; Convert harmonic bonds to morse potentials = morse = no ; NMR refinement stuff = ; Distance restraints type: No, Simple or Ensemble = disre = No ; Force weighting of pairs in one distance restraint: Equal or Conservative = disre_weighting = Equal ; Use sqrt of the time averaged times the instantaneous violation = disre_mixed = no disre_fc = 1000 disre_tau = 1.25 ; Output frequency for pair distances to energy file = nstdisreout = 100 ; Free energy control stuff = free_energy = no init_lambda = 0 delta_lambda = 0 sc-alpha = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff = acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = energygrp_excl = ; Electric fields = ; Format is number of terms (int) and for all terms an amplitude (real) = ; and a phase angle (real) = E-x = E-xt = E-y = 1 0.05 0.0 E-yt = E-z = E-zt = ; User defined thingies = user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 Any suggestions will be highly appreciated . Thank you very much. Yang _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
