[gmx-users] Empty trr file !!??

[ranqi zhu]

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. 

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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