/>/ > />/ Range checking error: > />/ Explanation: During neighborsearching, we assign each particle to a grid > />/ based on its coordinates. If your system contains collisions or parameter > />/ errors that give particles very high velocities you might end up with some > />/ coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot > />/ put these on a grid, so this is usually where we detect those errors. > />/ Make sure your system is properly energy-minimized and that the potential > />/ energy seems reasonable before trying again. > /Please follow the advice in the above two sentences. Check your structure. > > I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE > and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file > > Initiating Steepest Descents > Center of mass motion removal mode is Linear > We have the following groups for center of mass motion removal: > 0: rest, initial mass: 24594 > Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006 > Removing pbc first time > Done rmpbc > Steepest Descents: > Tolerance (Fmax) = 1.00000e+01 > Number of steps = 10000 > Grid: 10 x 10 x 20 cells > Configuring nonbonded kernels... > Testing AMD 3DNow support... not present. > Testing ia32 SSE support... present. > > > Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained > I get the following > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 1391229833052160.000000 (between atoms 655 and 657) rms 40665803128832.000000 > bonds that rotated more than 30 degrees: turn off the constraints > Hi David I did turn off the constraints and also made the starting structure unconstarined in the mdp file. The mdrun for position restrained gives Segmentation fault and the log file is shown below. Could you please suggest what could I do. I attached a pdb file in the earlier mail which has to be reviewed by the moderator of gmx list. Thanks Gaurav ------------------------------------------- Input Parameters: integrator = md nsteps = 1000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 bDomDecomp = FALSE decomp_dir = 0 nstcomm = 1 comm_mode = Linear nstcheckpoint = 1000 nstlog = 10000 nstxout = 0 nstvout = 250 nstfout = 0 nstenergy = 250 nstxtcout = 250 init_t = 0 delta_t = 0.002 xtcprec = 1000 nkx = 42 nky = 42 nkz = 84 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bUncStart = TRUE bShakeSOR = FALSE etc = Berendsen epc = Berendsen epctype = Isotropic tau_p = 20 ref_p (3x3): ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} compress (3x3): compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} andersen_seed = 815131 rlist = 1 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1 vdwtype = Cut-off rvdw_switch = 0 rvdw = 1 epsilon_r = 1 epsilon_rf = 1 tabext = 1 gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 implicit_solvent = No DispCorr = No fudgeQQ = 0.5 free_energy = no init_lambda = 0 sc_alpha = 0 sc_power = 1 sc_sigma = 0.3 delta_lambda = 0 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 dihre-tau = 0 nstdihreout = 100 em_stepsize = 0.01 em_tol = 10 niter = 20 fc_stepsize = 0 nstcgsteep = 1000 nbfgscorr = 10 ConstAlg = Lincs shake_tol = 1e-04 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: 51456 ref_t: 300 tau_t: 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 CPU= 0, lastcg= 8223, targetcg= 4112, myshift= 0 nsb->shift = 1, nsb->bshift= 0 Neighbor Search Blocks nsb->nodeid: 0 nsb->nnodes: 1 nsb->cgtotal: 8224 nsb->natoms: 24594 nsb->shift: 1 nsb->bshift: 0 Nodeid index homenr cgload workload 0 0 24594 8224 8224 Max number of graph edges per atom is 4 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: -0.000 Generated table with 1000 data points for Ewald. Tabscale = 500 points/nm Generated table with 1000 data points for LJ6. Tabscale = 500 points/nm Generated table with 1000 data points for LJ12. Tabscale = 500 points/nm Generated table with 500 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 500 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 500 data points for 1-4 LJ12. Tabscale = 500 points/nm Enabling SPC water optimization for 7441 molecules. 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 --- -------- -------- Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 150847 There are: 24594 Atoms Removing pbc first time Done rmpbc Started mdrun on node 0 Tue Mar 14 05:52:54 2006 Initial temperature: 430.169 K Step Time Lambda 0 0.00000 0.00000 Grid: 10 x 10 x 20 cells Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. There are 24594 atoms in your xtc output selection |
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