yes, I mean that when using the command "mdrun", the traj.xtc file is not ouput at all while the other files like "topol.tpr, ener.edr,md.log, mdout.mdp" are all output.
Hence, I just got confused about that. Yang ________________________________________ From: [email protected] [[email protected]] On Behalf Of Justin A. Lemkul [[email protected]] Sent: Friday, January 23, 2009 11:55 AM To: Gromacs Users' List Subject: Re: [gmx-users] why the trajectory file is not output He, Yang wrote: > 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 . > What files are produced? And again, are you referring to the absence of the trajectory *during* the simulation, or after? Which trajectory, .trr or .xtc, is missing? -Justin > 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 > -- ======================================== 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
