[gmx-users] Range Checking Error on EM

[Morgan Fairweather]

 Hello,
 
 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 ./#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)
 
 We have looked at the data to make sure that we havent created any overlapping atomic coordinates and also made sure the system charge is 0.
 
 Any suggestions as to the cause of the error?
 
 Morgan
 

			
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