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

[Jack Shultz]

I guess its the amber03 force field I'm having issues with. The
lysozyme tutorial works if I use -ff G43a2
Thanks

Jack

On Tue, Mar 17, 2009 at 8:01 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> Well, several tutorials use lysozyme, PDB 1AKI.  I would also recommend not
> using ffamber if you are running automated tests, since there are quirks
> with requiring specific nomenclature (for lysine, histidine, terminal
> residues, etc).
>
> -Justin
>
> Jack Shultz wrote:
>>
>> 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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>>
>>
>>
>
> --
> ========================================
>
> 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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