[gmx-users] Range Checking Error

Morgan Fairweather equalizer007700 at yahoo.com
Tue Dec 20 00:05:57 CET 2005


I am afraid my question got missed and so am reposting
it.  Further information that might be important is
that we created the structure with x2top in gromacs
3.2 and the energy minimization is being attempted in
version 3.3 :  
 I am trying to run a simulation on an infinite
silicon surface.  We built the structure from a unit
cell and used X2top with pbc option to generate a
framework for the itp file.  Bonds, angles and
dihedrals were generated in prodrg and the
ffG43a1bon.itp file was edited to include these
additions.  Currently, we are trying to run an energy
minimzation on the system and are running into  the
following error:
     Back Off! I just backed up mem1out.log to
     Getting Loaded...
     Reading file gem1out.tpr, VERSION 3.3 (single
     Loaded with Money
     Back Off! I just backed up mem1out.edr to
     Polak-Ribiere Conjugate Gradients:
        Tolerance (Fmax)   =  1.00000e+03
        Number of steps    =         5000
        F-max             =  1.13638e+08 on atom 59586
        F-Norm            =          nan
     Program mdrun, 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 -2147483648. It should have
been within [ 0 .. 11875 ]
     Please report this to the mailing list
(gmx-users at gromacs.org)
     "I'm Your Worst Nightmare" (Creep)
     Halting program mdrun
     gcq#38: "I'm Your Worst Nightmare" (Creep)

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