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hi! lina my script this.... please tell me where is 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 $MDP"<br><br>LAMBDA=0<br><br># A new directory will be created for each value of lambda and<br># at each step in the workflow for maximum organization.<br><br>mkdir Lambda_$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><br>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<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 $FREE_ENERGY/HIS1/topol.top -o min$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 $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3<br><br>mdrun -nt 8 -deffnm nvt$LAMBDA<br><br>echo "Constant volume equilibration complete."<br><br><br><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 $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr -maxwarn 3<br><br>mdrun -nt 8 -deffnm npt$LAMBDA<br><br>echo "Constant pressure equilibration complete."<br><br><br>#################<br># PRODUCTION MD #<br>#################<br>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 $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr -maxwarn 3<br><br>mdrun -nt 8 -deffnm md$LAMBDA<br><br>echo "Production MD complete."<br><br># End<br>echo "Ending. Job completed for lambda = $LAMBDA"<br><br><div><div id="SkyDrivePlaceholder"></div>> Date: Mon, 30 Jan 2012 13:54:18 +0800<br>> Subject: Re: [gmx-users] simulation killed<br>> From: lina.lastname@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900@hotm
ail.com> wrote:<br>> > hi again.... capacity of my harddisk 600 GB.... ı try again ..the program<br>> > gave me below message...<br>> ><br>> > Reading file md0.tpr, VERSION 4.5.4 (single precision)<br>> > Starting 8 threads<br>> ><br>> > NOTE: The load imbalance in PME FFT and solve is 1211%.<br>> > For optimal PME load balancing<br>> > PME grid_x (1152) and grid_y (1152) should be divisible by<br>> > #PME_nodes_x (8)<br>> > and PME grid_y (1152) and grid_z (1152) should be divisible by<br>> > #PME_nodes_y (1)<br>> ><br>> ><br>> > Making 1D domain decomposition 8 x 1 x 1<br>> > starting mdrun 'Protein in water'<br>> <br>> > 2500000 steps, 5000.0 ps.<br>> > ./job_0.sh: line 95: 15777 Killed
mdrun -nt 8 -deffnm<br>> <br>> What's inside your job_0.sh?<br>> <br>> something wrong your script.<br>> <br>> > md$LAMBDA<br>> ><br>> > Production MD complete.<br>> > Ending. Job completed for lambda = 0<br>> > mkiytak@babil:~/JOB1$<br>> ><br>> ><br>> > How can I solve this problem....thanks for your help.....<br>> ><br>> ><br>> ><br>> ><br>> ><br>> ><br>> ><br>> >> Date: Sun, 29 Jan 2012 10:43:53 -0600<br>> >> From: pcl@uab.edu<br>> >> To: gmx-users@gromacs.org<br>> >> Subject: Re: [gmx-users] simulation killed<br>> ><br>> >><br>> >> something killed your job but it wasn't gromacs.<br>> >> Your system has run time or memory requirements that your job exceeded.<br>> >><br>> >> On 2012-01-29 06:40:29PM +0200, mehmet kıytak wrote:<br>> >> > hi!
all<br>> >> ><br>> >> > ı have to a big problem..ı am doing free energy calculation for a ligand<br>> >> > (L<br>> >> > histidine ) when ı perform mdrun .. my simulation stop ... the program<br>> >> > gave<br>> >> > me this message..<br>> >> ><br>> >> > Reading file md0.tpr, VERSION 4.5.4 (single precision)<br>> >> > Starting 8 threads<br>> >> > Making 1D domain decomposition 8 x 1 x 1<br>> > & gt; > starting mdrun 'Protein in water'<br>> ><br>> >> > 2500000 steps, 5000.0 ps.<br>> >> > ./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm<br>> >> > md$LAMBDA<br>> >> > Production MD complete.<br>> >> > Ending. Job completed for lambda = 0<br>> >> > mkiytak@babil:~/JOB1$<br>> >> ><br>> >> ><br>> >> > my mdp file..<br>> >> >
;<br>> >> > ; 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>> >> > nstlog = 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 = EnerPres<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>> >> &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>> >> > 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>> ><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 ENGLİSH..<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>> >> Peter C. Lai | University of Alabama-Birmingham<br>> >> Programmer/Analyst | KAUL 752A<br>> >> Genetics, Div. 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>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search 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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