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lina ı didn't write this script.. script is on free energy tutorial 6 by justin a. lemkul<br>ı changed to my own business.. <span id="result_box" class="short_text" lang="en"><span class="hps">would like to calculate deltaGbinding for protein ligand complexes </span></span><br><br><div><div id="SkyDrivePlaceholder"></div>> Date: Mon, 30 Jan 2012 21:26:20 +0800<br>> Subject: Re: [gmx-users] simulation killed<br>> From: lina.lastname@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> On Mon, Jan 30, 2012 at 9:22 PM, Justin A. Lemkul <jalemkul@vt.edu> wrote:<br>> ><br>> ><br>> > lina wrote:<br>> >><br>> >> did you write this script yourself?<br>> >><br>> ><br>> > This script appears to be based on one that I provided in the free energy<br>> > tutorial, but there are some differences (including one of the mistakes you<br>> <br>> Your tutorials were well-written. I read some o
f them. but not this one. so ...<br>> <br>> > note below). It would be helpful if the OP explained what these simulations<br>> > were doing, as well as if they are attempting the tutorial or some other<br>> > different system.<br>> ><br>> > -Justin<br>> ><br>> ><br>> >> On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik <mehmet63900@hotmail.com><br>> >> wrote:<br>> >>><br>> >>> hi! lina my script this.... please tell me where is<br>> >>> wrong.......thanks....<br>> >>><br>> >>><br>> >>> #!/bin/bash<br>> >>><br>> >>> # Set some environment variables<br>> >>> FREE_ENERGY=/home/mkiytak/Free_Energy1<br>> >>> echo "Free energy home directory set to $FREE_ENERGY"<br>> >>><br>> >>> MDP=$FREE_ENERGY/MDP<br>> >>> echo ".mdp files are stored in $MDP"<br>> >
;>><br>> >>> LAMBDA=0<br>> >>><br>> >>> # A new directory will be created for each value of lambda and<br>> >>> # at each step in the workflow for maximum organization.<br>> >>><br>> >> Here add:<br>> >><br>> >> if [ -d "Lambda_$LAMBDA" ]; then<br>> >> rm -r Lambda_$LAMBDA<br>> >> fi<br>> >><br>> >>> mkdir Lambda_$LAMBDA<br>> >>> cd Lambda_$LAMBDA<br>> >>><br>> >>> #################################<br>> >>> # ENERGY MINIMIZATION 1: STEEP #<br>> >>> #################################<br>> >>> echo "Starting minimization for lambda = $LAMBDA..."<br>> >>><br>> >>> mkdir EM_1<br>> >>> cd EM_1<br>> >>><br>> >>> # Iterative calls to grompp and mdrun to run the simulations<br>> >>&g
t;<br>> >>> grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/HIS1/solv.gro -p<br>> >>> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3<br>> >>><br>> >>> mdrun -nt 8 -deffnm min$LAMBDA<br>> >>><br>> >>><br>> >>> ############################# ####<br>> >>> # ENERGY MINIMIZATION 2: L-BFGS #<br>> >>> #################################<br>> >>><br>> >>> cd ../<br>> >>> mkdir EM_2<br>> >>> cd EM_2<br>> >>><br>> >>> grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p<br>> >>> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3<br>> >>><br>> >>> # Run L-BFGS in serial (cannot be run in parallel)<br>> >>><br>> >>> mdrun -nt 1 -deffnm min$LAMBDA<br>> >>><br>> >>> echo "Minimization complete
."<br>> >>><br>> >>><br>> >>><br>> >>> #####################<br>> >>> # NVT EQUILIBRATION #<br>> >>> #####################<br>> >>> echo "Starting constant volume equilibration..."<br>> >>><br>> >>> cd ../<br>> >>> mkdir NVT<br>> >>> cd NVT<br>> >>><br>> >>> grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p<br>> >>> $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3<br>> >><br>> >><br>> >> One thing, do you use define = -DPOSRES in your nvt_0.mdp, if<br>> >> yes, you need take care where your posre.itp file stored.<br>> >><br>> >>> mdrun -nt 8 -deffnm nvt$LAMBDA<br>> >>><br>> >>> echo "Constant volume equilibration complete."<br>> >>><br>> >>><br>> &g
t;>><br>> >>> #####################<br>> >>> # NPT EQUILIBRATION #<br>> >>> #####################<br>> >>> echo "Starting constant pressure equilibration..."<br>> >>><br>> >>> cd ../<br>> >>> mkdir NPT<br>> >>> cd NPT<br>> >>><br>> >>> grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p<br>> >><br>> >><br>> >> Here "$ LAMBDA" --> "$LAMBDA", no space.<br>> >><br>> >>> $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr<br>> >>> -maxwarn 3<br>> >>><br>> >>> mdrun -nt 8 -deffnm npt$LAMBDA<br>> >>><br>> >>> echo "Constant pressure equilibration complete."<br>> >>><br>> >>><br>> >>> #################<br>> >>> # PRODUCTION MD #<br>> >>> #################<br>&
gt; >>> echo "Starting production MD simulation..."<br>> >>><br>> >>> cd ../<br>> >>> mkdir Production_MD<br>> >>> cd Production_MD<br>> >>><br>> >>> grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p<br>> >>> $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr<br>> >>> -maxwarn 3<br>> >>><br>> >>><br>> >>> mdrun -nt 8 -deffnm md$LAMBDA<br>> >>><br>> >>> echo "Production MD complete."<br>> >>><br>> >>> # End<br>> >>> echo "Ending. Job completed for lambda = $LAMBDA"<br>> >>><br>> >>>> Date: Mon, 30 Jan 2012 13:54:18 +0800<br>> >>>> Subject: Re: [gmx-users] simulation killed<br>> >>>> From: lina.lastname@gmail.com<br>> >>>> To: gmx-users@gromacs.org<br>> >>>
> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900@hotm<br>> >>>> ail.com><br>> >>>> wrote:<br>> >>>>><br>> >>>>> hi again.... capacity of my harddisk 600 GB.... ı try again ..the<br>> >>>>> program<br>> >>>>> gave me below message...<br>> >>>>><br>> >>>>> Reading file md0.tpr, VERSION 4.5.4 (single precision)<br>> >>>>> Starting 8 threads<br>> >>>>><br>> >>>>> NOTE: The load imbalance in PME FFT and solve is 1211%.<br>> >>>>> For optimal PME load balancing<br>> >>>>> PME grid_x (1152) and grid_y (1152) should be divisible by<br>> >>>>> #PME_nodes_x (8)<br>> >>>>> and PME grid_y (1152) and grid_z (1152) should be divisible by<br>> >
;>>>> #PME_nodes_y (1)<br>> >>>>><br>> >>>>><br>> >>>>> Making 1D domain decomposition 8 x 1 x 1<br>> >>>>> starting mdrun 'Protein in water'<br>> >>>>> 2500000 steps, 5000.0 ps.<br>> >>>>> ./job_0.sh: line 95: 15777 Killed mdrun -nt 8 -deffnm<br>> >>>><br>> >>>> What's inside your job_0.sh?<br>> >>>><br>> >>>> something wrong your script.<br>> >>>><br>> >>>>> md$LAMBDA<br>> >>>>><br>> >>>>> Production MD complete.<br>> >>>>> Ending. Job completed for lambda = 0<br>> >>>>> mkiytak@babil:~/JOB1$<br>> >>>>><br>> >>>>><br>> >>>>> How can I solve this problem....thanks for your
help.....<br>> >>>>><br>> >>>>><br>> >>>>><br>> >>>>><br>> >>>>><br>> >>>>><br>> >>>>><br>> >>>>>> Date: Sun, 29 Jan 2012 10:43:53 -0600<br>> >>>>>> From: pcl@uab.edu<br>> >>>>>> To: gmx-users@gromacs.org<br>> >>>>>> Subject: Re: [gmx-users] simulation killed<br>> >>>>>> something killed your job but it wasn't gromacs.<br>> >>>>>> Your system has run time or memory requirements that your job<br>> >>>>>> exceeded.<br>> >>>>>><br>> >>>>>> On 2012-01-29 06:40:29PM +0200, mehmet kıytak wrote:<br>> >>>>>>><br>> >>>>>>> hi! all<br>> >>>>>>><br>> >>>>>>> ı have to a big problem
..ı am doing free energy calculation for a<br>> >>>>>>> ligand<br>> >>>>>>> (L<br>> >>>>>>> histidine ) when ı perform mdrun .. my simulation stop ... the<br>> >>>>>>> program<br>> >>>>>>> gave<br>> >>>>>>> me this message..<br>> >>>>>>><br>> >>>>>>> Reading file md0.tpr, VERSION 4.5.4 (single precision)<br>> >>>>>>> Starting 8 threads<br>> >>>>>>> Making 1D domain decomposition 8 x 1 x 1<br>> >>>>><br>> >>>>> & gt; > starting mdrun 'Protein in water'<br>> >>>>><br>> >>>>>>> 2500000 steps, 5000.0 ps.<br>> >>>>>>> ./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm<br>> >>>>>>> md$LAMBDA<br>> >>>
>>>> Production MD complete.<br>> >>>>>>> Ending. Job completed for lambda = 0<br>> >>>>>>> mkiytak@babil:~/JOB1$<br>> >>>>>>><br>> >>>>>>><br>> >>>>>>> my mdp file..<br>> >>>>>><br>> >>>>>> &gt ;<br>> >>>>>>><br>> >>>>>>> ; Run control<br>> >>>>>>> integrator = sd ; Langevin dynamics<br>> >>>>>>> tinit = 0<br>> >>>>>>> dt = 0.002<br>> >>>>>>> nsteps = 2500000 ; 5 ns<br>> >>>>>>> nstcomm = 100<br>> >>>>>>> ; Output control<br>> >>>>>>> nstxout = 500<br>> >>>>>>> nstvout = 500<br>> >>>>>>> nstfout = 0<br>> >>>>>>> nstl
og = 500<br>> >>>>>>> nstenergy = 500<br>> >>>>>>> nstxtcout = 0<br>> >>>>>>> xtc-precision = 1000<br>> >>>>>>> ; Neighborsearching and short-range nonbonded interactions<br>> >>>>>>> nstlist = 10<br>> >>>>>>> ns_type = grid<br>> >>>>>>> pbc = xyz<br>> >>>>>>> rlist = 1.0<br>> >>>>>>> ; Electrostatics<br>> >>>>>>> coulombtype = PME<br>> >>>>>>> rcoulomb = 1.0<br>> >>>>>>> ; van der Waals<br>> >>>>>>> vdw-type = switch<br>> >>>>>>> rvdw-switch = 0.8<br>> >>>>>>> rvdw = 0.9<br>> >>>>>>> ; Apply long range dispersion corrections for Energy and Pressure<br>> >>>>>>> DispCorr = E
nerPres<br>> >>>>>>> ; Spacing for the PME/PPPM FFT grid<br>> >>>>>>> fourierspacing = 0.12<br>> >>>>>>> ; EWALD/PME/PPPM parameters<br>> >>>>>>> pme_order = 6<br>> >>>>>>> ewald_rtol = 1e-06<br>> >>>>>>> epsilon_surface = 0<br>> >>>>>>> optimize_fft = no<br>> >>>>>><br>> >>>>>> &g t; ; Temperature coupling<br>> >>>>>>><br>> >>>>>>> ; tcoupl is implicitly handled by the sd integrator<br>> >>>>>>> tc_grps = system<br>> >>>>>>> tau_t = 1.0<br>> >>>>>>> ref_t = 300<br>> >>>>>>> ; Pressure coupling is on for NPT<br>> >>>>>>> Pcoupl = Parrinello-Rahman<br>> >>>>>>> tau_p = 0.5<br>&
gt; >>>>>>> compressibility = 4.5e-05<br>> >>>>>>> ref_p = 1.0<br>> >>>>>>> ; Free energy control st uff<br>> >>>>>>> free_energy = yes<br>> >>>>>>> init_lambda = 0.00<br>> >>>>>>> delta_lambda = 0<br>> >>>>>>> foreign_lambda = 0.05<br>> >>>>>>> sc-alpha = 0.5<br>> >>>>>>> sc-power = 1.0<br>> >>>>>>> sc-sigma = 0.3<br>> >>>>>>> couple-moltype = system<br>> >>>>>>> couple-lambda0 = vdw ; only van der Waals interactions<br>> >>>>>>> couple-lambda1 = non e ; turn off everything, in this case<br>> >>>>>>> only vdW<br>> >>>>>>> couple-intramol = no<br>> >>>>>>> nstdhdl = 10<br>> >>>>>>
> ; Do not generate velocities<br>> >>>>>>> gen_vel = no<br>> >>>>>>> ; options for bonds<br>> >>>>>>> constraints = h-bonds ; we only have C-H bonds here<br>> >>>>>>> ; Type of constraint algorithm<br>> >>>>>>> constraint-algorithm = lincs<br>> >>>>>>> ; Constrain the starting configuration<br>> >>>>>>> ; since we are continuing from NPT<br>> >>>>>>> continuation = yes<br>> >>>>>>> ; Highest order in the expansion of the constraint coupling matrix<br>> >>>>>>> lincs-order = 12<br>> >>>>>>><br>> >>>>>>> PLEASE HELP ME... WHY THE PROGRAM STOP ( KİLLED) SORRY FOR BAD<br>> >>>>>>> ENGLİSH..<br>> >>>>>>> --<br>> >>>>>>> gm
x-users mailing list gmx-users@gromacs.org<br>> >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >>>>>>> Please search the archive at<br>> >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> >>>>>>> Please don't post (un)subscribe requests to the list. Use the<br>> >>>>>>> www interface or send it to gmx-users-request@gromacs.org.<br>> >>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> >>>>>><br>> >>>>>><br>> >>>>>> --<br>> >>>>>> =================== ===============================================<br>> >>>>>> Peter C. Lai | University of Alabama-Birmingham<br>> >>>>>> Programmer/Analyst | KAUL 752A<br>> >>>>>> Genetics, D
iv. of Research | 705 South 20th Street<br>> >>>>>> pcl@uab.edu | Birmingham AL 35294-4461<br>> >>>>>> (205) 690-0808 |<br>> >>>>>> ==================================================================<br>> >>>>>><br>> >>>>>> --<br>> >>>>>> gmx-users mailing list gmx-users@gromacs.org<br>> >>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >>>>>> Please search the archive at<br>> >>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> >>>>>> Please don't post (un)s ubscribe requests to the list. Use the<br>> >>>>>> www interface or send it to gmx-users-request@gromacs.org.<br>> >>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> >>>>><br>> >>>
>> --<br>> >>>>> gmx-users mailing list gmx-users@gromacs.org<br>> >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >>>>> Please search the archive at<br>> >>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> >>>>> Please don't post (un)subscribe requests to the list. Use the<br>> >>>>> www interface or send it to gmx-users-request@gromacs.org.<br>> >>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> >>>><br>> >>>> --<br>> >>>> gmx-users mailing list gmx-users@gromacs.org<br>> >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >>>> Please search the archive at<br>> >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> >>>> Please don't
post (un)subscribe requests to the list. Use the<br>> >>>> www interface or send it to gmx-users-request@gromacs.org.<br>> >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> >>><br>> >>> --<br>> >>> gmx-users mailing list gmx-users@gromacs.org<br>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >>> Please search the archive at<br>> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> >>> Please don't post (un)subscribe requests to the list. Use the<br>> >>> www interface or send it to gmx-users-request@gromacs.org.<br>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> ><br>> ><br>> > --<br>> > ========================================<br>> ><br>> > Justin A. Lemkul<br>> > Ph.D. Candidate<br>> > ICTAS
Doctoral Scholar<br>> > MILES-IGERT Trainee<br>> > Department of Biochemistry<br>> > Virginia Tech<br>> > Blacksburg, VA<br>> > jalemkul[at]vt.edu | (540) 231-9080<br>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> ><br>> > ========================================<br>> ><br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at<br>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www interface<br>> > or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please sear
ch the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div> </div></body>
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