[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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