On Mon, Jan 30, 2012 at 9:22 PM, Justin A. Lemkul <jalem...@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 <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.. >>>>>> >>>>>> > ; >>>>>>> >>>>>>> ; 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 >>>>>>> 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-requ...@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 >>>>>> p...@uab.edu | Birmingham AL 35294-4461 >>>>>> (205) 690-0808 | >>>>>> ================================================================== >>>>>> >>>>>> -- >>>>>> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> -- >>>> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> -- >>> gmx-users mailing list gmx-users@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-requ...@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 > > ======================================== > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. 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