[gmx-users] why the trajectory file is not output

He, Yang yang.he at mavs.uta.edu
Fri Jan 23 20:46:09 CET 2009


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: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
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
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--
========================================

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

========================================
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