[gmx-users] Range Checking Error

[David van der Spoel]

Morgan Fairweather wrote:
> 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?
Set the bonded force constant to 0.

> 
> 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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