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

[Jack Shultz]

Justin,

Can you suggest any pdb files I could use that are more simple? I've
been trying to use files from tutorials but it seems like are always
problematic.

Jack

On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
>
> -Justin
>
>> -------------------------------------------------------
>> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
Jack

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