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..
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