[gmx-users] Range checking error: only on double precision

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 18 00:20:14 CET 2009

Jack Shultz wrote:
> Hello,
> I just wanted to compare results between single and double precision.
> I reused the same parameters. Single works. Double caused errors on
> mdrun. Any idea why?
> http://hydrogenathome.org/result.php?resultid=1292662

I don't know why any of that worked at all.  You've got missing atoms and 
inconsistent naming (LYSH should be LYP if you really want a protonated lysine 
under the Amber ports, etc).  Did you give pdb2gmx -missing?  Otherwise, 
topology generation should have failed.

Especially troublesome:

System has non-zero total charge: -2.309866e+01

I would suggest running tests on a physically realistic system that has all 
atoms present and an integer charge.  Maybe single precision somehow overcame 
these topology problems, but I wouldn't trust any of the results.


> -------------------------------------------------------
> Program mdrun, VERSION 4.0.3
> Source code file: nsgrid.c, line: 357
> 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 .. 300 ]


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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