On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63...@hotmail.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 stuff >> > 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