It happens immediately at step 0., and the log file looks like :
Input Parameters: integrator = md nsteps = 20000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 0 comm_mode = Linear nstlog = 1000 nstxout = 600 nstvout = 600 nstfout = 600 nstenergy = 1000 nstxtcout = 1000 init_t = 0 delta_t = 0.001 xtcprec = 10000 nkx = 44 nky = 42 nkz = 120 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 1 epsilon_surface = -1 optimize_fft = FALSE ePBC = xyz bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = Nose-Hoover epc = No epctype = Isotropic tau_p = 1 ref_p (3x3): ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress (3x3): compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord_scaling = No posres_com (3): posres_com[0]= 0.00000e+00 posres_com[1]= 0.00000e+00 posres_com[2]= 0.00000e+00 posres_comB (3): posres_comB[0]= 0.00000e+00 posres_comB[1]= 0.00000e+00 posres_comB[2]= 0.00000e+00 andersen_seed = 815131 rlist = 1.1 rtpi = 0.05 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1.1 vdwtype = Cut-off rvdw_switch = 0 rvdw = 1.1 epsilon_r = 1 epsilon_rf = 1 tabext = 1 implicit_solvent = No gb_algorithm = Still gb_epsilon_solvent = 80 nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 DispCorr = EnerPres free_energy = no init_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 delta_lambda = 0 nwall = 0 wall_type = 9-3 wall_atomtype[0] = -1 wall_atomtype[1] = -1 wall_density[0] = 0 wall_density[1] = 0 wall_ewald_zfac = 3 pull = no disre = No disre_weighting = Conservative disre_mixed = FALSE dr_fc = 1000 dr_tau = 0 nstdisreout = 100 orires_fc = 0 orires_tau = 0 nstorireout = 100 dihre-fc = 1000 em_stepsize = 0.01 em_tol = 100 niter = 20 fc_stepsize = 0 nstcgsteep = 1000 nbfgscorr = 10 ConstAlg = Lincs shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 lincs_iter = 1 bd_fric = 0 ld_seed = 1993 cos_accel = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 0 12822 ref_t: 0 300 tau_t: 0 0.2 anneal: No No ann_npoints: 0 0 acc: 0 0 0 nfreeze: Y Y Y N N N energygrp_flags[ 0]: 1 0 energygrp_flags[ 1]: 0 0 efield-x: n = 0 efield-xt: n = 0 efield-y: n = 0 efield-yt: n = 0 efield-z: n = 0 efield-zt: n = 0 bQMMM = FALSE QMconstraints = 0 QMMMscheme = 0 scalefactor = 1 qm_opts: ngQM = 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Will do PME sum in reciprocal space. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Using the Ewald3DC correction for systems with a slab geometry. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ Y. In-Chul and M. L. Berkowitz Ewald summation for systems with slab geometry J. Chem. Phys. 111 (1999) pp. 3155-3162 -------- -------- --- Thank You --- -------- -------- Using a Gaussian width (1/beta) of 0.352179 nm for Ewald Cut-off's: NS: 1.1 Coulomb: 1.1 LJ: 1.1 System total charge: 0.000 Generated table with 4200 data points for Ewald. Tabscale = 2000 points/nm Generated table with 4200 data points for LJ6. Tabscale = 2000 points/nm Generated table with 4200 data points for LJ12. Tabscale = 2000 points/nm Enabling SPC water optimization for 2137 molecules. Configuring nonbonded kernels... Testing ia32 SSE2 support... present. Removing pbc first time ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- --- Thank You --- -------- -------- There are: 7699 Atoms Max number of connections per atom is 2 Total number of connections is 8548 Max number of graph edges per atom is 2 Total number of graph edges is 8548 Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 0.00e+00 Initial temperature: 304.27 K Started mdrun on node 0 Thu May 20 16:33:38 2010 Step Time Lambda 0 0.00000 0.00000 Grid: 5 x 5 x 14 cells Long Range LJ corr.: <C6> 1.1930e-03 Long Range LJ corr.: Epot -415.301, Pres: -51.4754, Vir: 415.301 Energies (kJ/mol) LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 6.44979e+04 -4.15301e+02 -1.00185e+05 -4.94669e+03 -4.10490e+04 Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) 1.72141e+04 -2.38349e+04 -2.38347e+04 3.22940e+02 1.36187e+04 On Thu, May 20, 2010 at 4:30 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sikandar Mashayak wrote: > >> Hi >> >> I have gromacs input files for md simulation, with these set up files >> (*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on one >> machine, but when I move it to other machine, I get segmentation fault when >> I do mdrun. Both the machines have exactly same types of installation of >> gromacs 4.0.7 . Also, I can run water tutorials successfully on both the >> machines. >> >> So what could be the source of segmentation fault? >> >> > MD is chaotic, so you may not get the same result every time you run a > simulation. Since you've not said how quickly the seg fault occurs it is > exceptionally hard to diagnose. Generally, seg faults with mdrun occur > because the system crashes from an instability. Without substantially more > information (system contents, .mdp settings, relevant log file output, etc) > there is not much more to suggest. > > -Justin > > thanks >> sikandar >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 >
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