I think your box is too small. try changing them. On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Nilesh Dhumal wrote: > >> 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. >> >> > Have you searched the website? You would have undoubtedly found this: > > > http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off > > You should also search the list archive. This problem shows up weekly, if > not daily sometimes. > > Is the problem in mdp file? >> > > Nothing seems obviously wrong. > > -Justin > > > 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 >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > _______________________________________________ > 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 > -- Yongchul "Greg" Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University
_______________________________________________ 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