[gmx-users] Range Checking Error

[David van der Spoel]

Gaurav Chopra wrote:
> Gaurav Chopra wrote:
>>/ Hi
> />/ 
> />/ I am doing a steepest descent for the initial mdrun for a peptide and it 
> />/ gives me the following error. Please advice.
> />/ 
> />/ Thanks
> />/ Gaurav
> />/ -------------------------------------------------------
> />/ 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.
> /Please follow the advice in the above two sentences. Check your structure.
> 
> I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
> and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file
> 
> Initiating Steepest Descents
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
>   0:  rest, initial mass: 24594
> Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
> Removing pbc first time
> Done rmpbc
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+01
>    Number of steps    =        10000
> Grid: 10 x 10 x 20 cells
> Configuring nonbonded kernels...
> Testing AMD 3DNow support... not present.
> Testing ia32 SSE support... present.
> 
> 
> Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
> I get the following
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 1391229833052160.000000 (between atoms 655 and 657) rms 40665803128832.000000
> bonds that rotated more than 30 degrees:

turn off the constraints

> 
> also segmentation fault.
> 
> Is there a different method to do energy minimization better as suggested in the range check error warning.
> 
> Thanks
> Gaurav
> 
> 
> 
>>/ 
> />/ Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
> />/ Please report this to the mailing list (gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>)
> />/ -------------------------------------------------------
> />/ 
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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 <http://www.gromacs.org/mailman/listinfo/gmx-users>	spoel at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>   http://folding.bmc.uu.se
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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://folding.bmc.uu.se
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