Re: [gmx-users] simulation killed

lina Mon, 30 Jan 2012 05:18:51 -0800

did you write this script yourself?

On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik <mehmet63...@hotmail.com> wrote:
> hi! lina my script this.... please tell me where is wrong.......thanks....
>
>
> #!/bin/bash
>
> # Set some environment variables
> FREE_ENERGY=/home/mkiytak/Free_Energy1
> echo "Free energy home directory set to $FREE_ENERGY"
>
> MDP=$FREE_ENERGY/MDP
> echo ".mdp files are stored in $MDP"
>
> LAMBDA=0
>
> # A new directory will be created for each value of lambda and
> # at each step in the workflow for maximum organization.
>
Here add:


if [ -d "Lambda_$LAMBDA" ]; then
        rm -r Lambda_$LAMBDA
fi

> mkdir Lambda_$LAMBDA
> cd Lambda_$LAMBDA
>
> #################################
> # ENERGY MINIMIZATION 1: STEEP  #
> #################################
> echo "Starting minimization for lambda = $LAMBDA..."
>
> mkdir EM_1
> cd EM_1
>
> # Iterative calls to grompp and mdrun to run the simulations
>
> grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/HIS1/solv.gro -p
> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>
> mdrun -nt 8 -deffnm min$LAMBDA
>
>
> ############################# ####
> # ENERGY MINIMIZATION 2: L-BFGS #
> #################################
>
> cd ../
> mkdir EM_2
> cd EM_2
>
> grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p
> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>
> # Run L-BFGS in serial (cannot be run in parallel)
>
> mdrun -nt 1 -deffnm min$LAMBDA
>
> echo "Minimization complete."
>
>
>
> #####################
> # NVT EQUILIBRATION #
> #####################
> echo "Starting constant volume equilibration..."
>
> cd ../
> mkdir NVT
> cd NVT
>
> grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p
> $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3

One thing, do you use  define         = -DPOSRES in your nvt_0.mdp, if
yes, you need take care where your posre.itp file stored.

>
> mdrun -nt 8 -deffnm nvt$LAMBDA
>
> echo "Constant volume equilibration complete."
>
>
>
> #####################
> # NPT EQUILIBRATION #
> #####################
> echo "Starting constant pressure equilibration..."
>
> cd ../
> mkdir NPT
> cd NPT
>
> grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p

Here "$ LAMBDA" --> "$LAMBDA", no space.

> $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr
> -maxwarn 3
>
> mdrun -nt 8 -deffnm npt$LAMBDA
>
> echo "Constant pressure equilibration complete."
>
>
> #################
> # PRODUCTION MD #
> #################
> echo "Starting production MD simulation..."
>
> cd ../
> mkdir Production_MD
> cd Production_MD
>
> grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p
> $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
> -maxwarn 3
>
>
> mdrun -nt 8 -deffnm md$LAMBDA
>
> echo "Production MD complete."
>
> # End
> echo "Ending. Job completed for lambda = $LAMBDA"
>
>> Date: Mon, 30 Jan 2012 13:54:18 +0800
>
>> Subject: Re: [gmx-users] simulation killed
>> From: lina.lastn...@gmail.com
>> To: gmx-users@gromacs.org
>
>>
>> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900@hotm ail.com>
>> wrote:
>> > hi again.... capacity of my harddisk 600 GB.... ı try again ..the
>> > program
>> > gave me below message...
>> >
>> > Reading file md0.tpr, VERSION 4.5.4 (single precision)
>> > Starting 8 threads
>> >
>> > NOTE: The load imbalance in PME FFT and solve is 1211%.
>> >       For optimal PME load balancing
>> >       PME grid_x (1152) and grid_y (1152) should be divisible by
>> > #PME_nodes_x (8)
>> >       and PME grid_y (1152) and grid_z (1152) should be divisible by
>> > #PME_nodes_y (1)
>> >
>> >
>> > Making 1D domain decomposition 8 x 1 x 1
>> > starting mdrun 'Protein in water'
>>
>> > 2500000 steps,   5000.0 ps.
>> > ./job_0.sh: line 95: 15777 Killed                   mdrun -nt 8 -deffnm
>>
>> What's inside your job_0.sh?
>>
>> something wrong your script.
>>
>> > md$LAMBDA
>> >
>> > Production MD complete.
>> > Ending. Job completed for lambda = 0
>> > mkiytak@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
>> > & gt; > starting mdrun 'Protein in water'
>> >
>> >> > 2500000 steps, 5000.0 ps.
>> >> > ./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm
>> >> > md$LAMBDA
>> >> > Production MD complete.
>> >> > Ending. Job completed for lambda = 0
>> >> > mkiytak@babil:~/JOB1$
>> >> >
>> >> >
>> >> > my mdp file..
>> >> &gt ;
>
>> >> > ; 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 st uff
>> >> > 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@gromacs.org
>> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> > Please search the archive at
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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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Re: [gmx-users] simulation killed

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