[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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