[gmx-users] simulation killed

[lina]

On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900 at hotmail.com> wrote:
> 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

What's inside your job_0.sh?

something wrong your script.

> 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
> & gt; > 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
>> &g t; ; 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 = non e ; 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..
>>
>> > --
>> > gmx-users mailing list gmx-users at gromacs.org
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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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>
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