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

[He, Yang]

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

; 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