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.lastn...@gmail.com > To: gmx-users@gromacs.org > > 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. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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