[gmx-users] simulation killed

[Peter C. Lai]

something killed your job but it wasn't gromacs.
Your system has run time or memory requirements that your job exceeded.

On 2012-01-29 06:40:29PM +0200, mehmet kıytak wrote:
> 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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-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
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