[gmx-users] simulation killed

lina lina.lastname at gmail.com
Mon Jan 30 14:26:20 CET 2012 

On Mon, Jan 30, 2012 at 9:22 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> lina wrote:
>>
>> did you write this script yourself?
>>
>
> This script appears to be based on one that I provided in the free energy
> tutorial, but there are some differences (including one of the mistakes you

Your tutorials were well-written. I read some of them. but not this one. so ...

> note below).  It would be helpful if the OP explained what these simulations
> were doing, as well as if they are attempting the tutorial or some other
> different system.
>
> -Justin
>
>
>> On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik <mehmet63900 at 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 = $LAMBDA"
>>>
>>>> Date: Mon, 30 Jan 2012 13:54:18 +0800
>>>> Subject: Re: [gmx-users] simulation killed
>>>> From: lina.lastname at gmail.com
>>>> To: gmx-users at gromacs.org
>>>> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900 at hotm
>>>> ail.com>
>>>> wrote:
>>>>>
>>>>> hi again.... capacity of my harddisk 600 GB.... ı try again ..the
>>>>> program
>>>>> gave me below message...
>>>>>
>>>>> Reading file md0.tpr, VERSION 4.5.4 (single precision)
>>>>> Starting 8 threads
>>>>>
>>>>> NOTE: The load imbalance in PME FFT and solve is 1211%.
>>>>>      For optimal PME load balancing
>>>>>      PME grid_x (1152) and grid_y (1152) should be divisible by
>>>>> #PME_nodes_x (8)
>>>>>      and PME grid_y (1152) and grid_z (1152) should be divisible by
>>>>> #PME_nodes_y (1)
>>>>>
>>>>>
>>>>> Making 1D domain decomposition 8 x 1 x 1
>>>>> starting mdrun 'Protein in water'
>>>>> 2500000 steps,   5000.0 ps.
>>>>> ./job_0.sh: line 95: 15777 Killed                   mdrun -nt 8 -deffnm
>>>>
>>>> What's inside your job_0.sh?
>>>>
>>>> something wrong your script.
>>>>
>>>>> md$LAMBDA
>>>>>
>>>>> Production MD complete.
>>>>> Ending. Job completed for lambda = 0
>>>>> mkiytak 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..
>>>>>>
>>>>>> &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 at 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
>>>>>> pcl at uab.edu | Birmingham AL 35294-4461
>>>>>> (205) 690-0808 |
>>>>>> ==================================================================
>>>>>>
>>>>>> --
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>>>>>
>>>>> --
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>>>>
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>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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