Hello, I am trying to equilibrate glucose in water using Gromacs 4.0.5 version. I am geting the error immidiately after the mdrun starts Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size p0_4238: p4_error: interrupt SIGSEGV: 11 Killed by signal 2.
Is the problem in mdp file? Nilesh Here is my pr.mdp file title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.002 ; ps ! nsteps = 200000 ; total 1.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME vdwtype = cut-off rcoulomb = 1.0 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = Berendsen tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = Berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 350.0 gen_seed = 173529 _______________________________________________ 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/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/mailing_lists/users.php
