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

[Justin A. Lemkul]

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

========================================