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$LAMBDA
Production MD complete.
Ending. Job completed for lambda = 0
mkiytak@babil:~/JOB1$
How can I solve this problem....thanks for your help.....
> Date: Sun, 29 Jan 2012 10:43:53 -0600
> From: p...@uab.edu
> To: gmx-users@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$LAMBDA
> > Production MD complete.
> > Ending. Job completed for lambda = 0
> > mkiytak@babil:~/JOB1$
> >
> >
> > 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
> p...@uab.edu | Birmingham AL 35294-4461
> (205) 690-0808 |
> ==================================================================
>
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