[gmx-users] simulation killed

[murat özçelik]

hi again.... capacity of my harddisk 600 GB.... ı try again ..the program gave me below message...
Reading file md0.tpr, VERSION 4.5.4 (single precision)
Starting 8 threads

NOTE: The load imbalance in PME FFT and solve is 1211%.
      For optimal PME load balancing
      PME grid_x (1152) and grid_y (1152) should be divisible by #PME_nodes_x (8)
      and PME grid_y (1152) and grid_z (1152) should be divisible by #PME_nodes_y (1)

Making 1D domain decomposition 8 x 1 x 1
starting mdrun 'Protein in water'
2500000 steps,   5000.0 ps.
./job_0.sh: line 95: 15777 Killed                  mdrun -nt 8 -deffnm md$LAMBDA
Production MD complete.
Ending. Job completed for lambda = 0
mkiytak at babil:~/JOB1$ 


How can I solve this problem....thanks for your help.....







> Date: Sun, 29 Jan 2012 10:43:53 -0600
> From: pcl at uab.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] simulation killed
> 
> 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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