[gmx-users] Range Checking Error
David van der Spoel
spoel at xray.bmc.uu.se
Tue Mar 14 17:53:23 CET 2006
Gaurav Chopra wrote:
> / />/ />/ />/ 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
set this to 1.0 or remove this setting
> 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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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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