[gmx-users] why the trajectory file is not output
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 23 20:55:20 CET 2009
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
>
> ========================================
> _______________________________________________
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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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