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 > 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 > ; 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 = none ; 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 [email protected] > 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 [email protected]. > 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 [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
