[gmx-users] simulation killed

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 30 14:22:52 CET 2012 


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 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
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> --
>>>>> =================== ===============================================
>>>>> 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 |
>>>>> ==================================================================
>>>>>
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> Please don't post (un)s ubscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
========================================

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

========================================

More information about the gromacs.org_gmx-users mailing list