[gmx-users] Empty trr file !!??
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 14 21:42:10 CEST 2008
ranqi zhu wrote:
> Dear Gromacs Users,
>
> I am using the most recent version 3.3.99. Iran my simulation with 20ns
> period for a total length of 300ns so thatI don't have to start from
> scratch if I have a unexpected crash duringthe simulation. It suppose to
> write out full precision trr file at theend of every 20ns for the next
> 20ns to start with. But I the trr filesI got are EMPTY!!
> Does anyone have any idea about this problem? mdp file is attached.
> Please help. Thanks in advance.
>
You have nstxout = 0, which means coordinates are never written.
-Justin
> Ranqi
>
> PS: I also encounter unexpected crash with V3.3.99. No error message found.
>
> This is my mdp file :
>
> ; 20ns NPT production
> integrator = sd
> ld_seed = -1
> ; start time and timestep in ps
> tinit = 0
> dt = 0.002
> nsteps = 10000000
> ; number of steps for center of mass motion removal =
> nstcomm = 100
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout = 0
> nstvout = 0
> nstfout = 0
> ; Output frequency for energies to log file and energy file
> nstlog = 50000 ; every 100 ps
> nstenergy = 50000
> ; Output frequency and precision for xtc file
> nstxtcout = 50000 ; every 100 ps
> xtc-precision = 10000
> xtc_grps = protein other
> energygrps = protein other
> ; 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 = 1.0
> domain-decomposition = no
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = pme
> ;rcoulomb-switch = 0
> rcoulomb = 1.0
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon-r = 1
> ; Method for doing Van der Waals
> vdw-type = switch
> ; cut-off lengths
> rvdw = 0.9
> rvdw-switch = 0.8
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.1
> ; 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 = 6
> ewald_rtol = 1e-06
> epsilon_surface = 0
> optimize_fft = no
> ; OPTIONS FOR TEMPERATURE COUPLING
> tc_grps = protein other
> tau_t = 1.0 1.0 ; Langevin friction constant (ps)
> ref_t = 300 300
> ;OPTIONS FOR PRESSURE COUPLING
> Pcoupl = berendsen
> pcoupltype = isotropic
> tau_p = 5.0 5.0
> compressibility = 4.5e-05
> ref_p = 1.0 1.0
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = no
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon-r = 1
> ; Method for doing Van der Waals
> vdw-type = switch
> ; cut-off lengths
> rvdw = 0.9
> rvdw-switch = 0.8
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.1
> ; 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 = 6
> ewald_rtol = 1e-06
> epsilon_surface = 0
> optimize_fft = no
> ; OPTIONS FOR TEMPERATURE COUPLING
> tc_grps = protein other
> tau_t = 1.0 1.0 ; Langevin friction constant (ps)
> ref_t = 300 300
> ;OPTIONS FOR PRESSURE COUPLING
> Pcoupl = berendsen
> pcoupltype = isotropic
> tau_p = 5.0 5.0
> compressibility = 4.5e-05
> ref_p = 1.0 1.0
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = no
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon-r = 1
> ; Method for doing Van der Waals
> vdw-type = switch
> ; cut-off lengths
> rvdw = 0.9
> rvdw-switch = 0.8
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.1
> ; 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 = 6
> ewald_rtol = 1e-06
> epsilon_surface = 0
> optimize_fft = no
> ; OPTIONS FOR TEMPERATURE COUPLING
> tc_grps = protein other
> tau_t = 1.0 1.0 ; Langevin friction constant (ps)
> ref_t = 300 300
> ;OPTIONS FOR PRESSURE COUPLING
> Pcoupl = berendsen
> pcoupltype = isotropic
> tau_p = 5.0 5.0
> compressibility = 4.5e-05
> ref_p = 1.0 1.0
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = no
> ; OPTIONS FOR BONDS
> constraints = hbonds
> ; Type of constraint algorithm
> constraint-algorithm = Lincs
> ; Do not constrain the start configuration
> unconstrained-start = yes
> ; Relative tolerance of shake
> shake-tol = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 12
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than =
> lincs-warnangle = 30
>
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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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