[gmx-users] version 3.3 - Range checking error

Joanne Hanna J.F.Hanna at warwick.ac.uk
Fri Nov 25 12:02:26 CET 2005

I have submitted the single tpr with mdrun_d to our queueing system but this may take some time. In the mean time the output from gmxcheck is:

                         :-)  G  R  O  M  A  C  S  (-:

                       GRowing Old MAkes el Chrono Sweat

                             :-)  VERSION 3.3  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2004, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                    :-)  gmxcheck_d (double precision)  (-:

Option     Filename  Type         Description
  -f       traj.xtc  Input, Opt.  Generic trajectory: xtc trr trj gro g96 pdb
 -f2       traj.xtc  Input, Opt.  Generic trajectory: xtc trr trj gro g96 pdb
 -s1       trys.tpr  Input, Opt!  Generic run input: tpr tpb tpa xml
 -s2       tryd.tpr  Input, Opt!  Generic run input: tpr tpb tpa xml
  -c      topol.tpr  Input, Opt.  Structure+mass(db): tpr tpb tpa gro g96 pdb
  -e       ener.edr  Input, Opt.  Generic energy: edr ene
 -e2      ener2.edr  Input, Opt.  Generic energy: edr ene
  -n      index.ndx  Input, Opt.  Index file

      Option   Type  Value  Description
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int      0  Set the nicelevel
     -vdwfac   real    0.8  Fraction of sum of VdW radii used as warning
      -bonlo   real    0.4  Min. fract. of sum of VdW radii for bonded atoms
      -bonhi   real    0.7  Max. fract. of sum of VdW radii for bonded atoms
        -tol   real  0.001  Relative tolerance for comparing real values
                            defined as 2*(a-b)/(|a|+|b|)
   -lastener string         Last energy term to compare (if not given all are
                            tested). It makes sense to go up until the

Reading file trys.tpr, VERSION 3.3 (single precision)
Reading file tryd.tpr, VERSION 3.3 (double precision)
comparing inputrec
comparing top
comparing idef
comparing ilist BONDS
comparing ilist G96BONDS
comparing ilist MORSE
comparing ilist CUBICBONDS
comparing ilist CONNBONDS
comparing ilist HARMONIC
comparing ilist FENEBONDS
comparing ilist ANGLES
comparing ilist G96ANGLES
comparing ilist CROSS_BOND_BOND
comparing ilist CROSS_BOND_ANGLE
comparing ilist UREY_BRADLEY
comparing ilist QANGLES
comparing ilist PDIHS
comparing ilist RBDIHS
comparing ilist FOURDIHS
comparing ilist IDIHS
comparing ilist PIDIHS
comparing ilist LJ14
comparing ilist COUL14
comparing ilist LJ_SR
comparing ilist BHAM
comparing ilist LJ_LR
comparing ilist BHAM_LR
comparing ilist DISPCORR
comparing ilist COUL_SR
comparing ilist COUL_LR
comparing ilist RF_EXCL
comparing ilist COUL_RECIP
comparing ilist POLARIZATION
comparing ilist WATERPOL
comparing ilist THOLE
comparing ilist POSRES
comparing ilist DISRES
comparing ilist DRVIOL
comparing ilist ORIRES
comparing ilist ORDEV
comparing ilist ANGRES
comparing ilist ANGRESZ
comparing ilist DIHRES
comparing ilist DIHVIOL
comparing ilist CONSTR
comparing ilist CONSTRNC
comparing ilist SETTLE
comparing ilist VSITE2
comparing ilist VSITE3
comparing ilist VSITE3FD
comparing ilist VSITE3FAD
comparing ilist VSITE3OUT
comparing ilist VSITE4FD
comparing ilist EQM
comparing ilist EPOT
comparing ilist EKIN
comparing ilist ETOT
comparing ilist TEMP
comparing ilist PRES
comparing ilist DV/DL
comparing ilist DK/DL
comparing atoms
comparing block excl
comparing block CGS
comparing block MOLS
comparing block SBLOCKS
comparing box
comparing boxv
comparing pcoupl_mu
comparing x
comparing v
v[ 1271] (-1.40864e-01 -7.22405e-01 -1.43657e-04) - (-1.40861e-01 -7.22389e-01 -1.43328e-04)
v[ 1284] (-1.34353e-01  2.07603e-01 -2.22835e-05) - (-1.34350e-01  2.07599e-01 -2.20149e-05)
v[ 1891] ( 2.03986e-01 -3.79670e-01 -3.00889e-04) - ( 2.03981e-01 -3.79661e-01 -3.00580e-04)
v[ 2284] (-9.92093e-01 -2.02473e-01  1.51159e-04) - (-9.92071e-01 -2.02468e-01  1.51346e-04)
v[ 4764] ( 1.29141e-03  2.77093e-03  5.68097e-02) - ( 1.28919e-03  2.76580e-03  5.68087e-02)
v[ 4904] ( 8.32858e-01 -1.37802e-04 -5.75344e-01) - ( 8.32840e-01 -1.37565e-04 -5.75331e-01)
v[ 6008] (-8.94540e-01 -7.27544e-01  2.45110e-04) - (-8.94520e-01 -7.27528e-01  2.45399e-04)
v[ 7499] (-1.63062e-01  7.14995e-05 -1.62903e-01) - (-1.63058e-01  7.16558e-05 -1.62899e-01)
v[ 8324] ( 1.14324e-01  7.67668e-05 -1.50298e-01) - ( 1.14321e-01  7.69088e-05 -1.50294e-01)
v[ 8735] (-6.06969e-01 -1.61352e-06 -4.49754e-02) - (-6.06955e-01 -1.45821e-06 -4.49744e-02)
v[ 9888] ( 2.64220e-02 -2.20640e-01 -2.11888e-04) - ( 2.64215e-02 -2.20635e-01 -2.12333e-04)
v[11453] ( 5.92208e-01 -1.71054e-01 -9.26887e-05) - ( 5.92195e-01 -1.71050e-01 -9.24038e-05)
v[11646] ( 1.42098e+00  5.65209e-05 -1.33867e-01) - ( 1.42095e+00  5.66801e-05 -1.33864e-01)
v[15593] ( 5.13614e-01 -8.98950e-03  3.61843e-04) - ( 5.13602e-01 -8.98964e-03  3.62277e-04)
v[17246] (-2.01884e-01  1.09552e+00  2.25234e-04) - (-2.01879e-01  1.09549e+00  2.25488e-04)
v[17903] (-2.50794e-01  2.32270e-03  7.71875e-04) - (-2.50788e-01  2.31883e-03  7.68736e-04)
v[20222] ( 5.66327e-01  7.53817e-05 -7.04423e-02) - ( 5.66314e-01  7.55094e-05 -7.04404e-02)
v[20730] (-2.30456e+00  2.06001e+00 -3.25712e-04) - (-2.30451e+00  2.05997e+00 -3.25327e-04)
v[21215] ( 1.61715e-01 -2.20110e-01 -1.29863e-04) - ( 1.61711e-01 -2.20105e-01 -1.29575e-04)
v[24034] (-6.46318e-03 -9.23752e-03  3.98703e+00) - (-6.47186e-03 -9.24895e-03  3.98694e+00)
v[24434] (-3.42673e-05  4.27094e-01  5.98853e-02) - (-3.42269e-05  4.27085e-01  5.98843e-02)
v[27530] (-6.17240e-02  7.34998e-01 -1.60463e-04) - (-6.17226e-02  7.34981e-01 -1.60202e-04)
v[29583] ( 4.06189e+00 -6.61411e-01  7.37444e-05) - ( 4.06180e+00 -6.61397e-01  7.40049e-05)
v[30560] ( 3.71091e-02 -8.11671e-05 -5.90703e-01) - ( 3.71087e-02 -8.10069e-05 -5.90690e-01)
v[33863] ( 2.72758e-01  1.69037e-01  2.72051e-04) - ( 2.72752e-01  1.69034e-01  2.72335e-04)
v[35519] (-8.15471e-01 -1.01503e-05  1.41510e-01) - (-8.15453e-01 -9.99258e-06  1.41507e-01)
v[39154] (-6.95194e-03 -4.23113e-03 -1.28670e+00) - (-6.94306e-03 -4.22680e-03 -1.28667e+00)
v[40886] ( 8.15019e-01  1.54104e-01 -3.50550e-06) - ( 8.15001e-01  1.54101e-01 -3.22000e-06)
v[42995] (-1.21166e-02  5.06068e-02  1.62131e-04) - (-1.21163e-02  5.06060e-02  1.62415e-04)
v[45362] (-1.79749e-05  1.29754e+00  2.00089e-01) - (-1.69773e-05  1.29751e+00  2.00084e-01)
v[45944] ( 1.46405e-01 -5.94038e-01 -2.81942e-03) - ( 1.46402e-01 -5.94024e-01 -2.83054e-03)
v[45945] (-3.25980e-03  1.52899e+00 -8.17517e-01) - (-3.31249e-03  1.52895e+00 -8.17499e-01)
v[46118] (-5.42803e-01 -1.08067e+00 -1.80423e-05) - (-5.42791e-01 -1.08064e+00 -1.78054e-05)
v[47300] (-6.85956e-02  2.53733e-01  1.35776e-04) - (-6.85940e-02  2.53728e-01  1.36062e-04)
v[49396] (-5.74291e-06  1.66057e+00  4.72148e-01) - (-5.63068e-06  1.66053e+00  4.72137e-01)
v[52143] ( 8.12834e-01 -1.20166e+00 -4.45708e-05) - ( 8.12816e-01 -1.20163e+00 -4.42905e-05)
v[54692] ( 8.63504e-02  2.49385e-01  1.85595e-04) - ( 8.63484e-02  2.49380e-01  1.85887e-04)
v[55339] (-5.59107e-01 -1.14537e+00 -2.13977e-04) - (-5.59094e-01 -1.14534e+00 -2.13735e-04)
v[56309] (-1.72899e-01  1.73651e-02 -1.77211e-04) - (-1.72895e-01  1.73645e-02 -1.76963e-04)
v[60452] (-3.99274e-02 -9.20381e-05  8.98222e-02) - (-3.99268e-02 -9.18780e-05  8.98204e-02)
v[62020] (-5.43588e-01  1.03238e-04  1.04118e+00) - (-5.43576e-01  1.03402e-04  1.04116e+00)
v[65744] ( 6.67981e-01 -8.54519e-01 -6.30703e-05) - ( 6.67966e-01 -8.54500e-01 -6.27991e-05)
v[67655] ( 4.12631e-01  4.89502e-05 -3.63763e-02) - ( 4.12622e-01  4.90976e-05 -3.63752e-02)

gcq#218: "I Was Born to Have Adventure" (F. Zappa)

Joanne Hanna
Department of Chemistry
University of Warwick

J.F.Hanna at warwick.ac.uk
>>> spoel at xray.bmc.uu.se 11/25/05 10:39 AM >>>
Joanne Hanna wrote:

>What I did was to use the files that were the output from a posres md 500ps run in v 3.2.1 (posres on protein, truc oct box spc water) and do grompp_d with v 3.3 and then mdrun_d with v3.3
Please compare the single and double precision tpr files using gmxcheck. 
In addition try to reproduce the problem by using the single precision 
tpr file with mdrun_d. If the tpr files are different there may be a 
problem with grompp, if they are identical there may be a problem with 
mdrun_d. Either way it is necessary to find out what is going on. If you 
can pinpoint the problem please submit a bugzilla.

>The hardware and os details are:
>node type: 1 x 1.6 GHz Itanium2 56-way SMP
>interconnect: SGI NUMAlink4
>OS: RedHat Enterprise Linux AS 3.0 / SGI ProPack
>All code was compiled with:
>using lmpi
>and enable threads for fftw
>I compiled fftw v 3 with the flags below, as there were no default flags for the intel compilers:
>export CFLAGS="-ftz -O3 -tpp2 -no-gcc"
>export FFLAGS="-ftz -O3 -tpp2"
>The only messages i got during during gromacs v3.3 compilation that i was unsure about are:
>checking dynamic linker characteristics... ifort: Command line warning: ignoring option '-p'; no argument required
>ifort: Command line error: no files specified; for help type "ifort -help"
>mknb_innerloop.c(362): warning #188: enumerated type mixed with another type
>                         mknb_func.coul=coulsave;
>                                       ^
>mknb_innerloop.c(363): warning #188: enumerated type mixed with another type
>                         mknb_func.vdw=vdwsave;
>                                      ^
>Hope this is what you were asking
>Joanne Hanna
>Department of Chemistry
>University of Warwick
>CV4 7AL
>J.F.Hanna at warwick.ac.uk
>>>>spoel at xray.bmc.uu.se 11/25/05 10:02 AM >>>
>Joanne Hanna wrote:
>>I have recently tried to re run a simualtion with gromacs v3.3 in double precision that I have managed to run in v3.2.1 single prescision and v3.3 single precision. This simulations is failing with the following error:
>Is this run with the same tpr file that works in single precision?
>What kind of hardware do you run on?
>>          Step           Time         Lambda
>>        104000      208.00000        0.00000
>>  Energies (kJ/mol)
>>      G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>>   8.43377e+03    3.79108e+03    2.53005e+03    3.13091e+02    5.79138e+04
>>       LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>>   1.38869e+05   -1.05323e+06   -1.68330e+05   -1.00971e+06    1.91922e+05
>>  Total Energy    Temperature Pressure (bar)
>>  -8.17790e+05    3.11754e+02    4.49698e+01
>>Program mdrun_d, VERSION 3.3
>>Source code file: nsgrid.c, line: 226
>>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.
>>Variable ci has value 5926. It should have been within [ 0 .. 5760 ]
>>Please report this to the mailing list (gmx-users at gromacs.org)
>>"Clickety Clickety Click" (System Manager From Hell)
>>Could anyone please explain to me what I have done wrong? Should I have re-do the entire process with the double preision? i.e. from starting structure, solvate minimise, md with posres on protein to equilib water and then run my simualtion?
>>Many thanks
>>Joanne Hanna
>>Department of Chemistry
>>University of Warwick
>>CV4 7AL
>>J.F.Hanna at warwick.ac.uk
>>gmx-users mailing list
>>gmx-users at gromacs.org
>>Please don't post (un)subscribe requests to the list. Use the 
>>www interface or send it to gmx-users-request at gromacs.org.

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://xray.bmc.uu.se/~spoel

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