[gmx-users] core dumped

[elham tazikeh]

Dear users
when i simulated Aspirin on Human serum albumin (pdb: 2i30)
in equilibration process (NVT), i encountered with below message and my
simulation stopped. i dont know why?









*pdfco at pdfco-X:~/Aspirin$ tail nvt.job-nex         int    0       Number of
random exchanges to carry out each                            exchange
interval (N^3 is one suggestion).  -nex                            zero or
not specified gives neighbor replica
exchange.-reseed      int    -1      Seed for replica exchange, -1 is
generate a seed-[no]ionize  bool   no      Do a simulation including the
effect of an X-Ray                            bombardment on your system*



*Reading file nvt.tpr, VERSION 4.6.5 (single precision)Using 1 MPI
thread[1]+  Segmentation fault      (core dumped) mdrun -v -deffnm nvt &>
nvt.job*





my *NVT.mdp* content was:

title  = Protein NVT equilibration
define  = -DPOSRES             ; position restrain the protein
; Run parameters
integrator = md               ; leap-frog integrator
nsteps  = 100000      ; 0.002 * 100000 = 200 ps
dt      = 0.002              ; 2 fs
; Output control
nstxout  = 1000              ; save coordinates every 0.2 ps
nstvout  = 1000              ; save velocities every 0.2 ps
nstenergy = 1000              ; save energies every 0.2 ps
nstlog  = 1000              ; update log file every 0.2 ps
; Bond parameters
continuation = no      ; first dynamics run
constraint_algorithm = lincs      ; holonomic constraints
constraints = all-bonds          ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1           ; accuracy of LINCS
lincs_order = 4           ; also related to accuracy
; Neighborsearching
ns_type  = grid              ; search neighboring grid cells
nstlist  = 5                  ; 10 fs
rlist  = 1.0      ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0      ; short-range electrostatic cutoff (in nm)
rvdw  = 1.0      ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME              ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4                  ; cubic interpolation
fourierspacing = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = v-rescale
tc-grps  = Protein_SAL SOL_CL ; two coupling groups - more accurate
tau_t  = 0.1 0.1             ; time constant, in ps
ref_t  = 310  310             ; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl  = no               ; no pressure coupling in NVT
; Periodic boundary conditions
pbc  = XYZ
; Dispersion correction
DispCorr = EnerPres             ; account for cut-off vdW scheme
; Velocity generation
gen_vel  = yes              ; assign velocities from Maxwell distribution
gen_temp = 300              ; temperature for Maxwell distribution
gen_seed = -1              ; generate a random seed



i really appriciate for your hint

regards