[gmx-users] simulation killed

[mehmet kıytak]

hi! all

ı have to a big problem..ı am doing free energy calculation for a ligand (L
histidine ) when ı perform mdrun .. my simulation stop ... the program gave
me this message..

Reading file md0.tpr, VERSION 4.5.4 (single precision)
Starting 8 threads
Making 1D domain decomposition 8 x 1 x 1
starting mdrun 'Protein in water'
2500000 steps,   5000.0 ps.
./job_0.sh: line 95: 15457 Killed                  mdrun -nt 8 -deffnm
md$LAMBDA
Production MD complete.
Ending. Job completed for lambda = 0
mkiytak at babil:~/JOB1$


my mdp file..

; Run control
integrator               = sd       ; Langevin dynamics
tinit                    = 0
dt                       = 0.002
nsteps                   = 2500000  ; 5 ns
nstcomm                  = 100
; Output control
nstxout                  = 500
nstvout                  = 500
nstfout                  = 0
nstlog                   = 500
nstenergy                = 500
nstxtcout                = 0
xtc-precision            = 1000
; Neighborsearching and short-range nonbonded interactions
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
; Electrostatics
coulombtype              = PME
rcoulomb                 = 1.0
; van der Waals
vdw-type                 = switch
rvdw-switch              = 0.8
rvdw                     = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; EWALD/PME/PPPM parameters
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
optimize_fft             = no
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps                  = system
tau_t                    = 1.0
ref_t                    = 300
; Pressure coupling is on for NPT
Pcoupl                   = Parrinello-Rahman
tau_p                    = 0.5
compressibility          = 4.5e-05
ref_p                    = 1.0
; Free energy control stuff
free_energy              = yes
init_lambda              = 0.00
delta_lambda             = 0
foreign_lambda           = 0.05
sc-alpha                 = 0.5
sc-power                 = 1.0
sc-sigma                 = 0.3
couple-moltype           = system
couple-lambda0           = vdw      ; only van der Waals interactions
couple-lambda1           = none     ; turn off everything, in this case
only vdW
couple-intramol          = no
nstdhdl                  = 10
; Do not generate velocities
gen_vel                  = no
; options for bonds
constraints              = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm     = lincs
; Constrain the starting configuration
; since we are continuing from NPT
continuation             = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 12

PLEASE HELP ME... WHY THE PROGRAM STOP  ( KİLLED)   SORRY FOR BAD ENGLİSH..
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