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Apparently your .log file has been truncated abnormally, but the energy values reported are clearly indicative of http://www.gromacs.org/Documentation/Terminology/Blowing_Up See that link for dealing with it. Mark
--- Begin Message ---This is what I got from .log file please help me find the error. ----------------------------------------------------------- Input Parameters: integrator = md nsteps = 50000 init_step = 0 ns_type = Grid nstlist = 5 ndelta = 2 nstcomm = 10 comm_mode = Linear nstlog = 100 nstxout = 100 nstvout = 100 nstfout = 0 nstcalcenergy = 5 nstenergy = 100 nstxtcout = 0 init_t = 0 delta_t = 0.002 xtcprec = 1000 nkx = 21 nky = 21 nkz = 21 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = Berendsen nsttcouple = 5 epc = No epctype = Isotropic nstpcouple = -1 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 = 1.6 rlistlong = 1.6 rtpi = 0.05 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1.6 vdwtype = Cut-off rvdw_switch = 0 rvdw = 1.6 epsilon_r = 1 epsilon_rf = 1 tabext = 1 implicit_solvent = No gb_algorithm = Still gb_epsilon_solvent = 80 nstgbradii = 1 rgbradii = 1 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 DispCorr = EnerPres free_energy = no init_lambda = 0 delta_lambda = 0 n_foreign_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 sc_sigma_min = 0.3 nstdhdl = 10 separate_dhdl_file = yes dhdl_derivatives = yes dh_hist_size = 1 dh_hist_spacing = 0.1 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 = 10 niter = 20 fc_stepsize = 0 nstcgsteep = 1000 em_stepsize = 0.01 em_tol = 10 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: 9213 ref_t: 300 tau_t: 0.1 anneal: No ann_npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp_flags[ 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 Initializing Domain Decomposition on 2 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2 cells with a minimum initial size of 0.000 nm Domain decomposition grid 2 x 1 x 1, separate PME nodes 0 PME domain decomposition: 2 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 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 Removing pbc first time Linking all bonded interactions to atoms The initial number of communication pulses is: X 1 The initial domain decomposition cell size is: X 1.62 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 The minimum size for domain decomposition cells is 1.600 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.99 Making 1D domain decomposition grid 2 x 1 x 1, home cell index 0 0 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 -------- -------- --- Thank You --- -------- -------- Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.51226 nm for Ewald Cut-off's: NS: 1.6 Coulomb: 1.6 LJ: 1.6 Long Range LJ corr.: <C6> 7.1048e-03 System total charge: 0.000 Generated table with 5200 data points for Ewald. Tabscale = 2000 points/nm Generated table with 5200 data points for LJ6. Tabscale = 2000 points/nm Generated table with 5200 data points for LJ12. Tabscale = 2000 points/nm Generated table with 5200 data points for 1-4 COUL. Tabscale = 2000 points/nm Generated table with 5200 data points for 1-4 LJ6. Tabscale = 2000 points/nm Generated table with 5200 data points for 1-4 LJ12. Tabscale = 2000 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing ia32 SSE2 support... present. Removing pbc first time Linking all bonded interactions to atoms The initial number of communication pulses is: X 1 The initial domain decomposition cell size is: X 1.62 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 The minimum size for domain decomposition cells is 1.600 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.99 aking 1D domain decomposition grid 2 x 1 x 1, home cell index 0 0 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 -------- -------- --- Thank You --- -------- -------- There are: 3072 Atoms Charge group distribution at step 0: 256 256 Grid: 4 x 4 x 4 cells Initial temperature: 300.045 K Started mdrun on node 0 Thu Aug 4 23:28:12 2011 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. LJ-14 Coulomb-14 5.10646e+02 9.74200e+01 6.47356e+01 1.49759e+04 2.42017e-01 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 6.17131e+06 -1.00056e+03 -2.29342e-01 -1.68456e-02 6.18596e+06 Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) 8.04863e+06 1.42346e+07 2.10143e+05 -9.69787e+02 1.49430e+07
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