[gmx-users] Range Checking Error

[Morgan Fairweather]

Hello,

Thank you for the help, I set pbc=full in the mdp file
and tried to analyze the results with g_energy. 
Unfortunately the simulation did not make it through 1
step so g_energy won't allow me to look at energy
terms.  Further, there is only 1 type of bond, an SI-O
bond so I am not as suspect of the bonded term.  Are
there any other ideas?

Morgan

>  Hello,
> 
> 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:
==================
did you sepcify
pbc = full
in the mdp file?
Check which energy term causes the high energy, I
would guess it is the 
bonded term.
==================
>  
>      Back Off! I just backed up mem1out.log to
> ./#mem1out.log.3#
>      Getting Loaded...
>      Reading file gem1out.tpr, VERSION 3.3 (single
> precision)
>      Loaded with Money
>  
>  
>      Back Off! I just backed up mem1out.edr to
> ./#mem1out.edr.3#
>      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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==================

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