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

He, Yang yang.he at mavs.uta.edu
Fri Jan 23 21:02:43 CET 2009


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: 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 11:55 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: 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to gmx-users-request at gromacs.org.
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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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