[gmx-users] simulation killed
mehmet kıytak
mehmet63900 at hotmail.com
Mon Jan 30 14:37:24 CET 2012
lina ı didn't write this script.. script is on free energy tutorial 6 by justin a. lemkul
ı changed to my own business.. would like to calculate deltaGbinding for protein ligand complexes
> Date: Mon, 30 Jan 2012 21:26:20 +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 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..
> >>>>>>
> >>>>>> > ;
> >>>>>>>
> >>>>>>> ; 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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> >>>>>>> www interface or send it to gmx-users-request 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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> >>>>
> >>>> --
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> >>>
> >>> --
> >>> gmx-users mailing list gmx-users at gromacs.org
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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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