[gmx-users] simulation killed
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 30 14:44:06 CET 2012
mehmet kıytak wrote:
> lina ı didn't write this script.. script is on free energy tutorial 6
> by justin a. lemkul
But you've adapted it and made at least one mistake, as was pointed out (an
erroneous space in a variable name).
> ı changed to my own business.. would like to calculate deltaGbinding for
> protein ligand complexes
>
Check the output written to the screen, logfile, or wherever else for
indications of an error message. A better approach would be to run each command
interactively to understand where it is failing. Then, once you have identified
the problem, proceed with a script that you can now have confidence in.
-Justin
> > 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 ! o f 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 $MDP"
> > &! gt ;>>
> > >>> LAMBDA=0
> > >>>
> > >>> # A new directory will be created for each value of lambda and
> > >>> # at each step in the workflow for maximum organization.
> > >>>
> > >> Here add:
> > >>
> > >> if [ -d "Lambda_$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
> > >>! ;&g t;
> > >>> 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 complet! e ."
> > >>>
> > >>>
> > >>>
> > >>> #####################
> > >>> # 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."
> > >>>
> > >>>
> > ! &g t;>>
> > >>> #####################
> > >>> # 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 #
> > >>> #################& gt; >>> 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 = $LAMBDA"
> > >>>
> > >>>> Date: Mon, 30 Jan 2012 13:54:18 +0800
> > >>>> Subject: Re: [gmx-users] simulation killed
> > >>>> From: lina.lastname at gmail.com
> > >>>> To: gmx-users at gromacs.org
> > >>>! ; > On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900 at hotm
> > >>>> ail.com>
> > >>>> wrote:
> > >>>>>
> > >>>>> hi again.... capacity of my harddisk 600 GB.... ı try again ..the
> > >>>>> program
> > >>>>> gave me below message...
> > >>>>>
> > >>>>> Reading file md0.tpr, VERSION 4.5.4 (single precision)
> > >>>>> Starting 8 threads
> > >>>>>
> > >>>>> NOTE: The load imbalance in PME FFT and solve is 1211%.
> > >>>>> For optimal PME load balancing
> > >>>>> PME grid_x (1152) and grid_y (1152) should be divisible by
> > >>>>> #PME_nodes_x (8)
> > >>>>> and PME grid_y (1152) and grid_z (1152) should be divisible by
> > &! gt ;>>>> #PME_nodes_y (1)
> > >>>>>
> > >>>>>
> > >>>>> Making 1D domain decomposition 8 x 1 x 1
> > >>>>> starting mdrun 'Protein in water'
> > >>>>> 2500000 steps, 5000.0 ps.
> > >>>>> ./job_0.sh: line 95: 15777 Killed mdrun -nt 8
> -deffnm
> > >>>>
> > >>>> What's inside your job_0.sh?
> > >>>>
> > >>>> something wrong your script.
> > >>>>
> > >>>>> md$LAMBDA
> > >>>>>
> > >>>>> Production MD complete.
> > >>>>> Ending. Job completed for lambda = 0
> > >>>>> mkiytak at babil:~/JOB1$
> > >>>>>
> > >>>>>
> > >>>>> How can I solve this problem....thanks for y! our 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 proble! m ..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$LAMBDA
> > >>&g! t; >>>> Production MD complete.
> > >>>>>>> Ending. Job completed for lambda = 0
> > >>>>>>> mkiytak at babil:~/JOB1$
> > >>>>>>>
> > >>>>>>>
> > >>>>>>> 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
> > >>>>>>> n! stl og = 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 = ! E nerPres
> > >>>>>>> ; 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& gt; >>>>>>> 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
> > >>>>>&! gt; > ; 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..
> > >>>>>>> --
> > >>>>>>> g! m x-users mailing list gmx-users at gromacs.org
> > >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > >>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>>>> ===================
> ===============================================
> > >>>>>> Peter C. Lai | University of Alabama-Birmingham
> > >>>>>> Programmer/Analyst | KAUL 752A
> > >>>>>> Genetics,! D iv. 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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> > >
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICT! AS 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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--
========================================
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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