[gmx-users]what is a segmentation fault?

[亓文鹏]

GROMACS Mailing List 
hi users:

what is a segmentation fault?
i think there must be some erros in the run parameters.
who can tell me the where and why? 
i want to simulate the process to pull the dickerson DNA (i get it from http:\\folding.stanford.edu\ffamber)
there is my mdrun.mdp
; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.003
nsteps                   = 50000
; For exact run continuation or redoing part of a run
init_step                = 0
; mode for center of mass motion removal
comm-mode                = None
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                = 
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
bd-temp                  = 300
bd-fric                  = 0
ld-seed                  = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol                    = 10
emstep                   = 0.01
; Max number of iterations in relax_shells
niter                    = 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep                   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep               = 1000
nbfgscorr                = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint            = 1000
; Output frequency for energies to log file and energy file
nstlog                   = 100
nstenergy                = 100
; Output frequency and precision for xtc file
nstxtcout                = 100
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                 = Protein    NA+
; Selection of energy groups
energygrps               = Protein     NA+   SOL
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
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                 = Cut-off
; cut-off lengths       
rvdw-switch              = 0
rvdw                     = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = No
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; 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
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no
tcoupl                   = No
Pcoupl                   = no
; OPTIONS FOR BONDS    
constraints              = none
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
unconstrained-start      = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = no
; Relative tolerance of shake
shake-tol                = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter               = 1
; 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
; Non-equilibrium MD stuff
acc-grps                 = 
accelerate               = 
freezegrps               = a_189_568
freezedim                = Y Y Y
cos-acceleration         = 0
thanks 
qi-wenpeng at mail.sdu.edu.cn
2005-8-14 
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