dear users, i wanted to simulate a DNA in a box of water using PME and run the calculation on a cluster with 16 nodes. i used the following mdp (see at the bottom of this mail) file and then submitted the job to our cluster. unfortunately i always get the following output: 50000 steps, 100.0 ps. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. Killed by signal 2. mdrun01 finished has anyone an idea of the reason for this problem. many thanks in advance greetings from hamburg joern this is my mdp-file: cpp = /usr/bin/cpp ; preprocessor define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 nsteps = 50000 nstcomm = 1 nstvout = 1000 nstxout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 pbc = xyz ; **************************************************** ; Berendsen temperature coupling is on ; **************************************************** tcoupl = berendsen tau_t = 0.1 1.0 0.5 0.5 0.5 0.5 tc_grps = Sol NA+ DGUA DADE DCYT DTHY ref_t = 100 100 100 100 100 100 ; *********************** ; Pressure coupling is on ; *********************** pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 100.0 gen_seed = 173529
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