I think this problem is not due to the disk space cause I check that it has a large space in the fold. I have tried some times but always the same results ,no trajectory files while the others are normal .
Thank you very much for your reply. Yang ________________________________________ From: [email protected] [[email protected]] On Behalf Of Justin A. Lemkul [[email protected]] Sent: Friday, January 23, 2009 11:42 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] why the trajectory file is not output He, Yang wrote: > 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 > During the simulation? Data is buffered, so you may not see immediate output. Or is the trajectory absent at the end of the simulation? That might indicate a problem with available disk space, depending on how large the file is. -Justin > ; 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 > -- ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ 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 _______________________________________________ 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
